Multiple platform build/check report for BioC 3.20 - CHECK results for biodbChebi on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4688
palomino8	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4284
lconway	macOS 12.7.1 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4455
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4404
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for biodbChebi on nebbiolo2

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

raw results

Summary

Package: biodbChebi

Version: 1.11.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz

StartedAt: 2024-07-23 21:28:04 -0400 (Tue, 23 Jul 2024)

EndedAt: 2024-07-23 21:30:11 -0400 (Tue, 23 Jul 2024)

EllapsedTime: 127.2 seconds

RetCode: 0

Status: OK

CheckDir: biodbChebi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-07-23 21:28:48.910][biodb::testContext]
biodb.INFO [2024-07-23 21:28:48.913][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:28:48.914][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-23 21:28:48.915][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:28:48.916][biodb::testContext]
biodb.INFO [2024-07-23 21:28:48.923][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:28:48.925][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-23 21:28:48.933][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:28:48.934][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-23 21:28:48.936][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-23 21:28:48.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.940][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-23 21:28:48.960][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-23 21:28:48.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.964][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-23 21:28:48.965][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-23 21:28:48.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.968][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-23 21:28:48.970][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-23 21:28:48.971][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-23 21:28:48.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.974][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-23 21:28:48.975][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-23 21:28:48.976][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-23 21:28:48.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.980][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-23 21:28:48.981][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-23 21:28:48.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.985][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-23 21:28:48.986][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-23 21:28:48.987][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-23 21:28:48.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.991][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-23 21:28:48.992][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-23 21:28:48.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:48.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:48.995][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-23 21:28:48.996][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-23 21:28:48.997][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-23 21:28:48.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:48.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.001][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:28:49.002][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-23 21:28:49.003][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-23 21:28:49.004][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-23 21:28:49.005][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-23 21:28:49.006][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-23 21:28:49.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.010][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-23 21:28:49.011][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-23 21:28:49.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.015][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-23 21:28:49.016][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-23 21:28:49.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.019][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-23 21:28:49.020][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-23 21:28:49.021][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.024][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-23 21:28:49.025][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-23 21:28:49.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.029][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-23 21:28:49.030][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-23 21:28:49.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.034][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:28:49.035][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-23 21:28:49.039][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-23 21:28:49.040][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.042][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.DEBUG[2024-07-23 21:28:49.043][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-23 21:28:49.044][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-23 21:28:49.045][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-23 21:28:49.046][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.052][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-23 21:28:49.089][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.113][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-23 21:28:49.114][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.115][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:28:49.116][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.117][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.117][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.118][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.119][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:28:49.120][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:28:49.121][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.122][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-23 21:28:49.123][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:28:49.124][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.125][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.125][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:28:49.125][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:28:49.125][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:28:49.125][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:28:49.125][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:28:49.126][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:28:49.127][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.128][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.129][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:28:49.130][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.130][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.131][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.132][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.133][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:28:49.134][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:28:49.135][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.136][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.137][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-23 21:28:49.138][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.139][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:28:49.140][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.141][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:28:49.142][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.143][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.144][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.145][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.146][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:28:49.147][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:28:49.147][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.148][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-23 21:28:49.149][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:28:49.150][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.151][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.152][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:28:49.152][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:28:49.152][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:28:49.152][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:28:49.152][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:28:49.153][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:28:49.154][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.154][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.155][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:28:49.156][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.157][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.158][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.159][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.160][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:28:49.160][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:28:49.161][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.162][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.163][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-23 21:28:49.165][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.166][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-23 21:28:49.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.168][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:28:49.168][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.169][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.170][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.171][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.172][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:28:49.173][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:28:49.174][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.175][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-23 21:28:49.176][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:28:49.176][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.177][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.178][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.179][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:28:49.180][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.181][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.182][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:28:49.182][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.184][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.185][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.186][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:28:49.187][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:28:49.188][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.188][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.189][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-23 21:28:49.191][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.192][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:28:49.193][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.194][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:28:49.195][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.196][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.196][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.197][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.198][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:28:49.199][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:28:49.200][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.201][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-23 21:28:49.202][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:28:49.203][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.204][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.204][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.205][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:28:49.206][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.207][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.208][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:28:49.209][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.210][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.210][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.211][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.212][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:28:49.213][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:28:49.214][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.215][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:28:49.219][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:28:49.219][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.225][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.228][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[2024-07-23 21:28:49.229][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.232][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[2024-07-23 21:28:49.233][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.248][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[2024-07-23 21:28:49.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.260][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[2024-07-23 21:28:49.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.265][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.289][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-23 21:28:49.294][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-23 21:28:49.295][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-23 21:28:49.296][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-23 21:28:49.298][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:28:49.299][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-23 21:28:49.300][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-23 21:28:49.301][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-23 21:28:49.303][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-23 21:28:49.304][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-23 21:28:49.305][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:28:49.307][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-23 21:28:49.308][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-23 21:28:49.309][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-23 21:28:49.310][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-23 21:28:49.312][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-23 21:28:49.313][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-23 21:28:49.314][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-23 21:28:49.315][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:28:49.317][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-23 21:28:49.318][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-23 21:28:49.319][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-23 21:28:49.320][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-23 21:28:49.322][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-23 21:28:49.323][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-23 21:28:49.324][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-23 21:28:49.326][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-23 21:28:49.327][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-23 21:28:49.328][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-23 21:28:49.329][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-23 21:28:49.331][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-23 21:28:49.332][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-23 21:28:49.333][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-23 21:28:49.334][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-23 21:28:49.336][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-23 21:28:49.337][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-23 21:28:49.343][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-23 21:28:49.344][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-23 21:28:49.345][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-23 21:28:49.347][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-23 21:28:49.348][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-23 21:28:49.349][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-23 21:28:49.350][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-23 21:28:49.352][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-23 21:28:49.353][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-23 21:28:49.354][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-23 21:28:49.356][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-23 21:28:49.357][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-23 21:28:49.358][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-23 21:28:49.359][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-23 21:28:49.361][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-23 21:28:49.362][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-23 21:28:49.363][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-23 21:28:49.364][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-23 21:28:49.366][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-23 21:28:49.367][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-23 21:28:49.368][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-23 21:28:49.370][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-23 21:28:49.371][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-23 21:28:49.372][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-23 21:28:49.373][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-23 21:28:49.375][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-23 21:28:49.376][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-23 21:28:49.377][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-23 21:28:49.379][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-23 21:28:49.380][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-23 21:28:49.381][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:28:49.382][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:28:49.384][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-23 21:28:49.385][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-23 21:28:49.386][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-23 21:28:49.388][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-23 21:28:49.389][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-23 21:28:49.390][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-23 21:28:49.391][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-23 21:28:49.393][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-23 21:28:49.394][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-23 21:28:49.395][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-23 21:28:49.397][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-23 21:28:49.398][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-23 21:28:49.399][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-23 21:28:49.400][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-23 21:28:49.402][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-23 21:28:49.407][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-23 21:28:49.409][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:28:49.412][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:28:49.413][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.415][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.425][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.447][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.DEBUG[2024-07-23 21:28:49.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.481][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[2024-07-23 21:28:49.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.484][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.488][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.499][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.503][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[2024-07-23 21:28:49.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.509][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[2024-07-23 21:28:49.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:28:49.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:49.516][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-23 21:28:49.525][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-23 21:28:49.527][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.528][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:28:49.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.532][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.533][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.533][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-23 21:28:49.534][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-23 21:28:49.535][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:28:49.536][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.537][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-23 21:28:49.538][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-23 21:28:49.539][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-23 21:28:49.540][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-23 21:28:49.541][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:28:49.541][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:28:49.541][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:28:49.542][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-23 21:28:49.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.543][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.544][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:28:49.545][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:28:49.546][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:28:49.547][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:28:49.548][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:28:49.548][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-23 21:28:49.549][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:28:49.550][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:28:49.550][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-23 21:28:49.551][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-23 21:28:49.551][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-23 21:28:49.557][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:28:49.559][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:28:49.560][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-23 21:28:49.561][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:28:49.563][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:28:49.564][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:28:49.592][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-23 21:28:49.593][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-23 21:28:49.598][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-23 21:28:49.602][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-23 21:28:49.606][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:28:49.607][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:28:49.609][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-23 21:28:49.610][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-23 21:28:49.619][biodb::testThat]
biodb.INFO [2024-07-23 21:28:49.620][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-07-23 21:28:49.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:49.622][biodb::testThat]
biodb.TRACE[2024-07-23 21:28:49.626][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-07-23 21:28:49.628][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:28:49.631][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:28:49.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:49.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:49.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:49.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:49.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:49.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:49.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:49.667][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.669][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.670][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.688][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:49.689][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:49.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.690][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.716][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:49.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.720][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:49.721][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:49.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.723][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:49.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.728][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:49.729][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:49.730][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.731][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:49.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:49.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.736][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.737][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.738][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.739][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.740][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.744][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:49.745][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:49.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.747][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.748][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:49.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:49.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.752][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:49.753][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:49.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.755][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.756][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:49.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:49.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.760][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:49.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:49.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.762][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:49.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:49.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.767][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:49.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:49.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.770][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:49.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.775][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:49.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:49.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.778][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.779][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:49.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:49.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:49.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.786][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.787][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:49.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:49.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:49.869][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-07-23 21:28:49.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:49.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:49.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:49.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:49.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:49.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:49.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:49.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:49.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:49.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-23 21:28:49.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-23 21:28:49.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.920][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-23 21:28:49.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-23 21:28:49.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.924][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-23 21:28:49.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-23 21:28:49.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-23 21:28:49.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-23 21:28:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:49.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:49.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:49.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:49.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:49.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.025][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.026][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.028][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.080][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.082][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.108][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.109][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.111][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.112][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.123][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.131][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.135][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.136][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.137][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.138][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.160][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.161][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.163][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.185][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.186][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.188][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.200][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.204][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.208][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.212][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.213][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.215][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.215][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.226][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.231][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.234][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.238][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.239][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.241][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.242][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.257][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.261][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.265][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.266][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.267][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.268][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.293][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.296][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.297][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.299][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.300][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.319][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.323][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.324][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.326][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.352][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.353][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.355][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.368][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.369][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.371][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.376][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.377][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.379][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.383][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.384][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.386][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.390][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.391][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.393][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.398][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.399][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.401][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.405][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.406][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.407][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.408][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.412][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.413][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.415][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.419][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.420][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.422][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.426][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.427][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.429][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.433][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.434][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.435][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.439][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.440][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.442][ef$get] fields variable is a list.
biodb.INFO [2024-07-23 21:28:50.449][biodb::testThat]
biodb.INFO [2024-07-23 21:28:50.450][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-23 21:28:50.451][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:50.451][biodb::testThat]
biodb.DEBUG[2024-07-23 21:28:50.465][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-07-23 21:28:50.472][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:28:50.477][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-07-23 21:28:50.478][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:50.479][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-07-23 21:28:50.480][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:28:50.510][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:28:50.511][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:28:50.513][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:50.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:50.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:50.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:50.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:50.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:50.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:50.524][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.525][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.526][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.526][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.547][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.549][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.550][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.552][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:50.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:50.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.556][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.556][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.558][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.560][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:50.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:50.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.563][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.564][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.566][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.571][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.572][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.574][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.575][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.579][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.580][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.583][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:50.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.587][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:50.588][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.590][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.591][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:50.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.595][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.596][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.598][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.599][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.603][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.604][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.606][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.611][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:50.612][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.614][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.615][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:50.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:50.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.619][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.620][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.622][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:50.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:50.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:50.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:50.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:50.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:50.666][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-07-23 21:28:50.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-23 21:28:50.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-23 21:28:50.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-23 21:28:50.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-23 21:28:50.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-23 21:28:50.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-23 21:28:50.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-23 21:28:50.686][biodb::testThat]
biodb.INFO [2024-07-23 21:28:50.687][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-23 21:28:50.688][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:50.689][biodb::testThat]
biodb.TRACE[2024-07-23 21:28:50.691][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.693][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.694][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:50.695][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-07-23 21:28:50.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.734][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:50.740][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-07-23 21:28:50.745][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-23 21:28:50.765][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:50.780][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-23 21:28:50.782][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:50.783][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-23 21:28:50.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:28:50.808][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:50.809][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-23 21:28:50.811][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:50.812][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-23 21:28:50.814][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-07-23 21:28:50.824][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.825][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:50.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.827][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.828][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.831][ef$get] fields variable is a list.
biodb.INFO [2024-07-23 21:28:50.835][biodb::testThat]
biodb.INFO [2024-07-23 21:28:50.836][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-07-23 21:28:50.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:50.838][biodb::testThat]
biodb.TRACE[2024-07-23 21:28:50.860][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.864][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:50.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:50.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:50.933][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:28:50.936][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:50.938][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-23 21:28:50.939][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:50.940][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-07-23 21:28:50.954][biodb::testThat]
biodb.INFO [2024-07-23 21:28:50.955][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-07-23 21:28:50.956][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:50.957][biodb::testThat]
biodb.TRACE[2024-07-23 21:28:50.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:50.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:50.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.983][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:50.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.990][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:50.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:50.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:50.998][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-23 21:28:50.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-23 21:28:51.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.002][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-23 21:28:51.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-23 21:28:51.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.006][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-23 21:28:51.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-23 21:28:51.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.009][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-23 21:28:51.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-23 21:28:51.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:51.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:51.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:51.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:51.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.039][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:51.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:51.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:51.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:51.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:51.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:51.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:51.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:51.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.054][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-23 21:28:51.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-23 21:28:51.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.058][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-23 21:28:51.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-23 21:28:51.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.061][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-23 21:28:51.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-23 21:28:51.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:51.065][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-23 21:28:51.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-23 21:28:51.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:51.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-23 21:28:51.075][biodb::testThat]
biodb.INFO [2024-07-23 21:28:51.076][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-23 21:28:51.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:51.078][biodb::testThat]
biodb.INFO [2024-07-23 21:28:51.085][biodb::testThat]
biodb.INFO [2024-07-23 21:28:51.086][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-23 21:28:51.087][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:51.088][biodb::testThat]
biodb.INFO [2024-07-23 21:28:51.096][biodb::testThat]
biodb.INFO [2024-07-23 21:28:51.098][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-23 21:28:51.098][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:51.099][biodb::testThat]
biodb.DEBUG[2024-07-23 21:28:51.103][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-07-23 21:28:51.735][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-07-23 21:28:52.866][biodb::testThat]
biodb.INFO [2024-07-23 21:28:52.868][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-23 21:28:52.870][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:52.871][biodb::testThat]
biodb.DEBUG[2024-07-23 21:28:53.332][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-07-23 21:28:53.761][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:53.763][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:53.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:53.765][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:53.766][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:53.767][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:53.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:53.769][ef$get] fields variable is a list.
biodb.INFO [2024-07-23 21:28:53.771][biodb::testThat]
biodb.INFO [2024-07-23 21:28:53.773][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-07-23 21:28:53.774][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:28:53.775][biodb::testThat]
biodb.TRACE[2024-07-23 21:28:53.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:53.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:53.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:53.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:53.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:53.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:53.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:53.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:53.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:53.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:53.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:53.905][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:28:53.909][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:53.911][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-23 21:28:53.912][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:53.913][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-23 21:28:53.994][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:28:53.998][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:54.000][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-23 21:28:54.002][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:54.003][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-07-23 21:28:54.020][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-23 21:28:54.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-23 21:28:54.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:54.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:54.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:54.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:54.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:54.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:54.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:54.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:54.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:54.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:54.046][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:54.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:54.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:54.058][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:28:54.062][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:54.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-23 21:28:54.065][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:54.067][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-23 21:28:54.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:54.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:54.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:54.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:54.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:54.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:54.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:54.081][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-07-23 21:28:54.149][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:28:54.151][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-07-23 21:28:54.153][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:28:54.154][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:28:54.156][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:28:54.157][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:28:54.158][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:28:54.158][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:28:54.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:54.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:54.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:54.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:54.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:54.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:54.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:54.171][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-07-23 21:28:54.174][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:28:54.175][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:28:54.176][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-07-23 21:28:54.565][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-07-23 21:28:54.963][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:28:54.965][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-07-23 21:28:54.979][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-07-23 21:28:54.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-07-23 21:28:54.983][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:28:54.984][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:28:54.985][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:28:54.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:54.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:54.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:54.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:54.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:54.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:54.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:54.998][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:54.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.001][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.006][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:55.007][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:55.008][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.009][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:55.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:55.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.014][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:55.015][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:55.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.017][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.019][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:55.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:55.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.023][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:55.024][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:55.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.026][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:55.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:55.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.031][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:55.032][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:55.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.033][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:55.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:55.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.038][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:55.039][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:55.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.041][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.042][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:55.044][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.045][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.058][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:55.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.062][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:55.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:55.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:55.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:55.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.071][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:55.072][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:55.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.073][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:55.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:55.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.079][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:55.080][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:55.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.082][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.083][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:55.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:55.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.087][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:55.088][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:55.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.090][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.091][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:55.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:55.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:55.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:55.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:55.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:55.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:55.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:55.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:55.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:55.132][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-07-23 21:28:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:55.153][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:28:55.156][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:55.157][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-23 21:28:55.158][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:55.160][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-23 21:28:55.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:55.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:55.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:55.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:55.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:55.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:55.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:55.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:55.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:55.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:55.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:55.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:55.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:55.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:55.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:55.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:55.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:55.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:55.206][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-07-23 21:28:55.207][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:28:55.209][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-07-23 21:28:55.210][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:28:55.211][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:28:55.212][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:28:55.213][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:28:55.214][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:28:55.215][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:28:55.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:55.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:55.236][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:55.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:55.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:55.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:55.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:55.244][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-07-23 21:28:55.259][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:28:55.260][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:28:55.274][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-07-23 21:28:55.666][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-07-23 21:28:56.059][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:28:56.063][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-07-23 21:28:56.071][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-07-23 21:28:56.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-07-23 21:28:56.081][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:28:56.084][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:28:56.086][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:28:56.090][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:56.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:56.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:56.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:56.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:56.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:56.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:56.113][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.115][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.117][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.125][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:56.127][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:56.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.129][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.131][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:56.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:56.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.136][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:56.137][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:56.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.139][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.141][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:56.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:56.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.145][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:56.146][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:56.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.148][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:56.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:56.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.154][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:56.155][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:56.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.157][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:56.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:56.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.162][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:56.163][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:56.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.165][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.167][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:56.168][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.170][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.171][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:56.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.175][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:56.176][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:56.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.178][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:56.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:56.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.184][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:56.185][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:56.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.187][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:56.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:56.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.192][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:56.193][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:56.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.195][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.200][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:56.201][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:56.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.214][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.215][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:56.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:56.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:56.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:56.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:56.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:56.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:56.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:56.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:56.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:56.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:56.260][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-07-23 21:28:56.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:56.295][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:28:56.298][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:28:56.299][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-23 21:28:56.301][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:28:56.302][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-23 21:28:56.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:56.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:56.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:56.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:56.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:56.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:56.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:56.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:56.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:56.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:56.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:56.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:56.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:56.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:56.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:56.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:56.334][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:56.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:56.336][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-07-23 21:28:56.337][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:28:56.339][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-07-23 21:28:56.340][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:28:56.341][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:28:56.342][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:28:56.343][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:28:56.344][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:28:56.345][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:28:56.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:56.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:56.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:56.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:56.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:56.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:56.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:56.358][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-07-23 21:28:56.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:28:56.362][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:28:56.363][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-07-23 21:28:56.765][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-07-23 21:28:57.174][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:28:57.179][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-07-23 21:28:57.186][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-07-23 21:28:57.191][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-07-23 21:28:57.193][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:28:57.195][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:28:57.198][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:28:57.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:57.203][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:57.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:57.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:57.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:57.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:57.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:57.224][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.226][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.229][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.259][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:57.260][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:57.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.262][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.264][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:57.265][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:57.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.266][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.268][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:57.269][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:57.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.271][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.272][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:57.273][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:57.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.275][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.277][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:57.278][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:57.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.280][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.281][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:57.282][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.284][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.285][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:57.287][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:57.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.288][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.290][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:57.291][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:57.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.293][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.294][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:57.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:57.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.299][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:57.300][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:57.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.302][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.303][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:57.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:57.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.307][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:57.308][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:57.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.310][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:57.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:57.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:57.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:57.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:57.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:57.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:57.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:57.352][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-07-23 21:28:57.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:57.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:57.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:57.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:57.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:57.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:57.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:57.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:57.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:57.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:57.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:57.384][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-07-23 21:28:57.385][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:28:57.387][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-07-23 21:28:57.388][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:28:57.389][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:28:57.390][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:28:57.391][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:28:57.392][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:28:57.393][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:28:57.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:57.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:57.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:57.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:57.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:57.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:57.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:57.407][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-07-23 21:28:57.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:28:57.410][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:28:57.412][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-07-23 21:28:57.814][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-07-23 21:28:58.237][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:28:58.241][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-07-23 21:28:58.246][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-07-23 21:28:58.251][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-07-23 21:28:58.254][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:28:58.256][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:28:58.259][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:28:58.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:58.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:58.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:58.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:58.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:58.284][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:58.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:58.287][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.288][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.290][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.296][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:58.297][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:58.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.298][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.300][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:58.301][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:58.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.302][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.304][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:58.305][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:58.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.307][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.308][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:58.309][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:58.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.311][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:58.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:58.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.315][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.316][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:58.317][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.319][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.320][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:58.321][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:58.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.323][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.324][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:58.325][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:58.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.327][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.328][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:58.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:58.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.332][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:58.333][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:58.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.335][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.336][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:58.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:58.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.340][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:58.341][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:58.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.343][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:58.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:58.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:58.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:58.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:58.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:58.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:58.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:58.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:58.382][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-07-23 21:28:58.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:58.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:58.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:58.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:58.402][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:58.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:58.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:58.408][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:58.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:58.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:58.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:58.412][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-07-23 21:28:58.413][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:28:58.414][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-07-23 21:28:58.416][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:28:58.417][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:28:58.418][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:28:58.419][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:28:58.420][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:28:58.421][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:28:58.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:58.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:58.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:58.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:58.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:58.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:58.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:58.433][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-07-23 21:28:58.436][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:28:58.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:28:58.438][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-07-23 21:28:58.826][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-07-23 21:28:59.217][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:28:59.220][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-07-23 21:28:59.230][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-07-23 21:28:59.238][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-07-23 21:28:59.239][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:28:59.241][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:28:59.242][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:28:59.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:59.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:59.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:59.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:59.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:59.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:59.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:28:59.256][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.258][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.259][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.265][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:28:59.266][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:28:59.267][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.268][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.270][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:28:59.271][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:28:59.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.272][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.274][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:28:59.275][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:28:59.276][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.277][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.278][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:28:59.279][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:28:59.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.281][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.282][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:59.283][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:28:59.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.285][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.286][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:28:59.287][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.289][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.290][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:59.291][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:28:59.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.293][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.294][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:59.295][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:59.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.297][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:28:59.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:28:59.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.303][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:59.304][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:59.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.305][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.307][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:28:59.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:28:59.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.311][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:28:59.312][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:28:59.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.313][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:59.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:59.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:59.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:59.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:28:59.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:28:59.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:28:59.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:28:59.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:59.353][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-07-23 21:28:59.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:28:59.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:28:59.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:28:59.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:28:59.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:59.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:59.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:59.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:59.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:59.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:59.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:59.391][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-07-23 21:28:59.393][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:28:59.395][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-07-23 21:28:59.396][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:28:59.398][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:28:59.399][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:28:59.400][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:28:59.401][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:28:59.402][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:28:59.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:28:59.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:28:59.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:28:59.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:28:59.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:28:59.416][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:28:59.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:28:59.418][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.INFO [2024-07-23 21:28:59.440][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-07-23 21:28:59.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:28:59.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:28:59.444][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-07-23 21:28:59.835][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-07-23 21:29:00.249][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:00.252][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-07-23 21:29:00.255][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-07-23 21:29:00.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-07-23 21:29:00.260][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:00.261][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:00.263][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:00.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:00.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:00.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:00.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:00.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:00.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:00.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:00.276][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.280][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.285][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:00.286][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:00.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.288][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.290][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:00.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:00.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.294][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:00.295][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:00.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.297][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.299][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:00.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:00.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.303][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:00.304][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:00.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.306][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:00.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:00.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.311][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:00.312][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:00.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.314][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.315][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:00.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:00.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.319][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:00.320][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:00.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.322][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.324][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:00.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:00.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.328][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:00.329][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.331][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.332][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:00.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.336][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:00.337][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:00.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.339][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.340][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:00.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:00.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.344][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:00.345][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:00.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.347][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:00.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:00.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.353][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:00.354][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:00.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.356][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.357][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:00.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:00.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.361][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:00.362][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:00.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.364][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.365][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:00.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:00.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:00.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:00.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:00.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:00.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:00.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:00.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:00.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:00.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:00.408][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-07-23 21:29:00.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.413][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:00.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:00.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:00.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:00.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:00.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:00.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:00.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:00.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:00.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:00.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:00.439][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-07-23 21:29:00.440][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:00.441][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-07-23 21:29:00.443][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:00.444][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:00.445][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:00.446][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:00.446][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:00.447][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:00.450][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:00.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:00.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:00.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:00.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:00.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:00.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:00.460][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-07-23 21:29:00.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:00.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:00.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-07-23 21:29:00.853][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-07-23 21:29:01.254][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:01.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-07-23 21:29:01.265][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-07-23 21:29:01.271][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-07-23 21:29:01.274][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:01.276][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:01.279][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:01.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:01.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:01.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:01.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:01.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:01.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:01.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:01.305][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.306][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.309][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.317][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:01.318][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:01.320][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.321][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.323][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:01.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:01.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.328][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:01.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:01.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.331][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.333][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:01.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:01.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.337][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:01.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:01.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.340][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:01.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:01.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.345][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:01.346][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:01.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.348][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:01.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:01.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.353][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:01.354][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:01.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.356][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.357][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:01.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:01.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.361][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:01.361][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.363][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.364][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:01.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.368][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:01.369][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:01.370][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.371][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:01.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.376][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:01.377][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:01.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.379][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:01.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:01.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.384][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:01.385][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:01.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.387][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.388][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:01.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:01.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.392][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:01.393][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:01.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.395][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.396][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:01.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:01.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:01.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:01.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:01.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:01.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:01.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:01.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:01.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:01.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:01.446][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-07-23 21:29:01.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:01.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:01.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:01.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:01.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:01.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:01.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:01.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:01.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:01.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:01.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:01.468][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-07-23 21:29:01.469][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:01.470][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-07-23 21:29:01.472][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:01.473][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:01.474][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:01.475][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:01.476][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:01.476][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:01.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:01.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:01.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:01.485][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:01.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:01.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:01.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:01.489][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-07-23 21:29:01.492][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:01.493][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:01.494][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-07-23 21:29:01.881][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-07-23 21:29:02.270][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-07-23 21:29:02.272][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-07-23 21:29:02.274][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-07-23 21:29:02.277][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-07-23 21:29:02.279][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-07-23 21:29:02.280][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:02.282][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:02.283][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:02.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:02.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:02.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:02.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:02.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:02.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:02.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:02.296][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.297][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.298][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.304][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:02.305][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:02.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.306][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.308][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:02.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:02.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.312][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:02.313][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:02.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.315][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.316][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:02.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.320][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:02.321][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:02.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.323][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.324][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:02.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:02.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.328][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:02.329][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:02.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.330][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.331][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:02.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:02.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.335][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:02.336][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:02.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.338][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.339][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:02.344][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.346][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.348][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:02.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.352][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:02.353][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:02.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.355][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:02.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:02.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.361][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:02.362][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:02.363][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.364][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.365][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:02.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:02.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.392][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:02.393][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:02.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.395][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.396][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:02.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:02.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.400][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:02.402][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:02.403][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.404][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.405][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:02.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:02.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:02.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:02.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:02.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:02.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.417][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:02.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:02.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:02.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:02.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:02.449][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-07-23 21:29:02.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:02.458][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:02.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:02.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:02.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:02.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:02.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:02.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:02.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:02.470][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:02.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:02.472][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-07-23 21:29:02.473][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:02.475][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-07-23 21:29:02.476][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:02.478][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:02.479][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:02.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:02.481][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:02.482][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:02.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:02.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:02.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:02.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:02.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:02.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:02.494][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[2024-07-23 21:29:02.495][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-07-23 21:29:02.498][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:02.499][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:02.501][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-07-23 21:29:02.887][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-07-23 21:29:03.280][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:03.285][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-07-23 21:29:03.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-07-23 21:29:03.298][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-07-23 21:29:03.302][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:03.305][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:03.308][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:03.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:03.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:03.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:03.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:03.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:03.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:03.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:03.335][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.336][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.340][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.348][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:03.349][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:03.350][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.352][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.353][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:03.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:03.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.358][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:03.359][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:03.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.361][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.363][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:03.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:03.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.367][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:03.368][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:03.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.370][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.371][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:03.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:03.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.375][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:03.382][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:03.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.387][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:03.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:03.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.392][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:03.393][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:03.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.395][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.396][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:03.397][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.399][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.400][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:03.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.404][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:03.405][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:03.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.407][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:03.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:03.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.412][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:03.413][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:03.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.415][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:03.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:03.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.420][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:03.421][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:03.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.422][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.424][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:03.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:03.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.427][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:03.428][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:03.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.430][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.431][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:03.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:03.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.435][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:03.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:03.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:03.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:03.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:03.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:03.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:03.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:03.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:03.472][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-07-23 21:29:03.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:03.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:03.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:03.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:03.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:03.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:03.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:03.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:03.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:03.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:03.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:03.494][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-07-23 21:29:03.495][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:03.497][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-07-23 21:29:03.498][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:03.499][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:03.500][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:03.501][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:03.502][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:03.503][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:03.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:03.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:03.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:03.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:03.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:03.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:03.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:03.516][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-07-23 21:29:03.519][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:03.519][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:03.521][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-07-23 21:29:03.907][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-07-23 21:29:04.325][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:04.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-07-23 21:29:04.338][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-07-23 21:29:04.344][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-07-23 21:29:04.347][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:04.350][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:04.353][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:04.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:04.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:04.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:04.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:04.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:04.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:04.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:04.380][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.382][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.400][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.407][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:04.408][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:04.409][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.410][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.412][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:04.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:04.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.416][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:04.417][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:04.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.419][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.420][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:04.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:04.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.424][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:04.425][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:04.426][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.427][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.428][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:04.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:04.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.433][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:04.435][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:04.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.437][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:04.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:04.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.444][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:04.445][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:04.446][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.447][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.448][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:04.449][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.451][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.452][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:04.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.456][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:04.457][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:04.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.459][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:04.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:04.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.464][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:04.465][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:04.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.467][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.468][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:04.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:04.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.472][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:04.473][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:04.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.475][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.477][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:04.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:04.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.480][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:04.482][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:04.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.484][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:04.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:04.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:04.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:04.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:04.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:04.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:04.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:04.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:04.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:04.530][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-07-23 21:29:04.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:04.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:04.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:04.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:04.544][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:04.545][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:04.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:04.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:04.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:04.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:04.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:04.556][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-07-23 21:29:04.557][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:04.558][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-07-23 21:29:04.560][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:04.561][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:04.562][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:04.563][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:04.564][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:04.565][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:04.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:04.569][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:04.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:04.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:04.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:04.576][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:04.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:04.578][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-07-23 21:29:04.587][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:04.588][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:04.590][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-07-23 21:29:04.990][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-07-23 21:29:05.387][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:05.391][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-07-23 21:29:05.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-07-23 21:29:05.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-07-23 21:29:05.400][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:05.402][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:05.403][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:05.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:05.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:05.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:05.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:05.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:05.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:05.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:05.419][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.420][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.422][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.428][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:05.429][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:05.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.431][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.432][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:05.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:05.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.436][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:05.438][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:05.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.441][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.443][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:05.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:05.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.468][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:05.470][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:05.473][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.475][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:05.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:05.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.483][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:05.485][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:05.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.487][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:05.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:05.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.494][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:05.495][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:05.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.498][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.499][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:05.501][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.502][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.503][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.505][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:05.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:05.511][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:05.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.514][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:05.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:05.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.522][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:05.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:05.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.527][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:05.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:05.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.537][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:05.539][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:05.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.542][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.544][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:05.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:05.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.550][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:05.552][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:05.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.554][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:05.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:05.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:05.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:05.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:05.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:05.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:05.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:05.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:05.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:05.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:05.615][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-07-23 21:29:05.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:05.629][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:05.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:05.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:05.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:05.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:05.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:05.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:05.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:05.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:05.742][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-07-23 21:29:05.744][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:05.746][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-07-23 21:29:05.747][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:05.774][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:05.776][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:05.777][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:05.779][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:05.780][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:05.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:05.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:05.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:05.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:05.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:05.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:05.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:05.819][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-07-23 21:29:05.822][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:05.823][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:05.849][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-07-23 21:29:06.335][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-07-23 21:29:06.727][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:06.730][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-07-23 21:29:06.733][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-07-23 21:29:06.735][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-07-23 21:29:06.737][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:06.738][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:06.739][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:06.741][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:06.742][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:06.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:06.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:06.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:06.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:06.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:06.753][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.754][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.755][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.761][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:06.762][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:06.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.763][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.765][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:06.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:06.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.769][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:06.770][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:06.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.772][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.773][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:06.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:06.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:06.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:06.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.780][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:06.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:06.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.785][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:06.786][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:06.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.788][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.789][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:06.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:06.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.793][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:06.794][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:06.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.795][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.797][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:06.798][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.800][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.801][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:06.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.805][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:06.806][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:06.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.808][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:06.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:06.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.813][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:06.814][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:06.815][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.815][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:06.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:06.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.821][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:06.822][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:06.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.824][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.825][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:06.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:06.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.829][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:06.830][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:06.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.832][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.833][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:06.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:06.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:06.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:06.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:06.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:06.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:06.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:06.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:06.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:06.889][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-07-23 21:29:06.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:06.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:06.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:06.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:06.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:06.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:06.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:06.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:06.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:06.911][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:06.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:06.913][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-07-23 21:29:06.914][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:06.916][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-07-23 21:29:06.917][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:06.919][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:06.920][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:06.921][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:06.922][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:06.923][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:06.925][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:06.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:06.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:06.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:06.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:06.935][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:06.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:06.937][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-07-23 21:29:06.940][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:06.941][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:06.943][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-07-23 21:29:07.332][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-07-23 21:29:07.741][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:07.744][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-07-23 21:29:07.749][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-07-23 21:29:07.752][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-07-23 21:29:07.754][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:07.756][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:07.758][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:07.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:07.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:07.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:07.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:07.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:07.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:07.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:07.775][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.778][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.784][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:07.785][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:07.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.787][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:07.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:07.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.793][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:07.794][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:07.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.796][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:07.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:07.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.802][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:07.803][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:07.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.805][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.806][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:07.807][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:07.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.809][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.811][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:07.812][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:07.813][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.815][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:07.816][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.818][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.826][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:07.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.833][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:07.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:07.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.837][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:07.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.843][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:07.844][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:07.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.846][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.848][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:07.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:07.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.853][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:07.854][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:07.855][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.856][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.857][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:07.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:07.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.861][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:07.863][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:07.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.865][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:07.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:07.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:07.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:07.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:07.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:07.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:07.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:07.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:07.938][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-07-23 21:29:07.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:07.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:07.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:07.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:07.951][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:07.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:07.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:07.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:07.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:07.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:07.961][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[2024-07-23 21:29:07.962][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-07-23 21:29:07.963][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:07.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-07-23 21:29:07.967][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:07.968][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:07.969][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:07.970][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:07.971][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:07.972][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:07.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:07.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:07.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:07.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:07.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:07.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:07.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:07.986][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-07-23 21:29:07.989][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:07.990][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:07.992][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-07-23 21:29:08.379][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-07-23 21:29:08.770][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:08.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-07-23 21:29:08.778][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-07-23 21:29:08.782][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-07-23 21:29:08.785][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:08.787][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:08.789][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:08.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:08.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:08.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:08.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:08.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:08.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:08.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:08.807][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.808][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.810][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.815][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:08.817][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:08.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.820][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:08.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:08.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.827][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:08.828][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:08.831][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.833][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:08.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:08.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.840][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:08.842][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:08.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.844][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.846][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:08.848][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:08.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.850][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.851][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:08.853][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:08.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.855][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.857][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:08.858][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.860][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.861][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:08.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.865][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:08.866][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:08.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.868][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:08.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:08.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.874][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:08.875][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:08.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.877][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:08.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:08.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.899][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:08.901][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:08.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.904][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.906][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:08.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:08.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.911][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:08.912][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:08.914][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.915][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:08.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:08.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:08.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:08.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:08.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:08.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:08.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:08.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:08.972][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-07-23 21:29:08.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:08.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:08.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:08.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:08.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:08.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:08.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:09.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:09.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:09.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:09.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:09.006][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-07-23 21:29:09.008][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:09.011][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-07-23 21:29:09.014][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:09.016][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:09.017][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:09.018][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:09.019][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:09.020][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:09.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:09.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:09.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:09.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:09.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:09.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:09.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:09.038][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-07-23 21:29:09.043][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:09.044][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:09.045][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-07-23 21:29:09.451][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-07-23 21:29:09.878][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:09.881][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-07-23 21:29:09.886][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-07-23 21:29:09.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-07-23 21:29:09.892][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:09.894][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:09.895][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:09.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:09.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:09.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:09.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:09.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:09.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:09.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:09.917][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:09.918][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:09.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.920][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:09.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:09.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.927][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:09.928][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:09.929][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.931][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.932][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:09.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:09.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.939][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:09.941][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:09.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.944][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:09.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:09.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.954][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:09.956][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:09.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.960][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:09.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:09.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.970][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:09.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:09.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.975][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:09.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:09.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:09.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:09.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.005][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:10.008][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:10.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.011][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.012][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:10.013][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.015][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.017][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:10.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.023][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:10.024][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:10.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.028][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:10.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:10.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.037][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:10.038][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:10.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.040][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:10.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:10.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.045][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:10.046][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:10.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.048][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.049][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:10.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:10.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.054][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:10.056][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:10.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.059][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.061][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:10.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:10.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:10.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:10.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:10.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:10.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:10.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:10.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:10.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:10.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:10.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:10.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:10.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:10.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:10.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:10.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:10.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:10.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:10.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:10.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:10.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:10.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:10.129][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-07-23 21:29:10.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:10.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:10.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:10.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:10.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:10.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:10.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:10.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:10.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:10.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:10.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:10.164][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-07-23 21:29:10.165][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:10.168][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-07-23 21:29:10.170][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:10.171][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:10.173][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:10.174][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:10.175][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:10.176][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:10.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:10.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:10.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:10.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:10.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:10.191][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:10.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:10.193][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-07-23 21:29:10.197][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:10.198][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:10.200][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-07-23 21:29:10.643][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-07-23 21:29:11.068][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:11.074][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-07-23 21:29:11.082][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-07-23 21:29:11.088][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-07-23 21:29:11.091][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:11.094][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:11.096][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:11.100][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:11.101][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:11.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:11.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:11.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:11.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:11.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:11.128][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.131][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.134][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.145][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:11.148][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:11.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.184][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.187][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:11.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:11.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.196][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:11.197][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:11.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.199][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.201][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:11.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:11.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.205][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:11.206][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:11.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.208][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:11.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:11.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.217][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:11.218][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:11.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.222][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.224][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:11.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:11.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.231][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:11.233][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:11.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.236][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.238][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:11.240][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.244][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.246][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:11.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.253][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:11.254][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:11.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.257][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:11.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:11.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.264][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:11.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:11.266][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.267][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:11.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:11.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.276][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:11.277][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:11.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.280][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.283][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:11.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:11.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.290][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:11.292][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:11.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.296][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.298][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:11.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:11.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:11.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:11.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:11.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:11.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:11.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:11.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:11.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:11.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:11.373][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-07-23 21:29:11.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:11.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:11.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:11.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:11.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:11.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:11.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:11.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:11.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:11.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:11.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:11.405][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-07-23 21:29:11.407][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:11.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-07-23 21:29:11.412][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:11.415][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:11.417][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:11.419][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:11.421][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:11.423][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:11.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:11.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:11.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:11.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:11.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:11.446][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:11.447][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.DEBUG[2024-07-23 21:29:11.450][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-07-23 21:29:11.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:11.457][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:11.460][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-07-23 21:29:11.896][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-07-23 21:29:12.321][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:12.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-07-23 21:29:12.356][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-07-23 21:29:12.360][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-07-23 21:29:12.363][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:12.365][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:12.367][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:12.369][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:12.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:12.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:12.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:12.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:12.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:12.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:12.390][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.392][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.394][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.400][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:12.401][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:12.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.403][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.405][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:12.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:12.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.411][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:12.413][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:12.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.416][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.419][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:12.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:12.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.427][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:12.429][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:12.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.433][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:12.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:12.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.443][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:12.445][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:12.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.448][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:12.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:12.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.459][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:12.461][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:12.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.464][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.467][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:12.469][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.472][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.474][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:12.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.481][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:12.483][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:12.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.487][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:12.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:12.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.496][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:12.498][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:12.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.502][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.505][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:12.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:12.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.513][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:12.514][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:12.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.518][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.520][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:12.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:12.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.527][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:12.528][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:12.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.532][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.534][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:12.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:12.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:12.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:12.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:12.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:12.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:12.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:12.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.572][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:12.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:12.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:12.584][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-07-23 21:29:12.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:12.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:12.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:12.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:12.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:12.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:12.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:12.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:12.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:12.614][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:12.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:12.625][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-07-23 21:29:12.628][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:12.632][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-07-23 21:29:12.634][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:12.636][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:12.637][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:12.639][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:12.641][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:12.643][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:12.647][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:12.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:12.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:12.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:12.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:12.665][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:12.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:12.670][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-07-23 21:29:12.678][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:12.680][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:12.684][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-07-23 21:29:13.109][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-07-23 21:29:13.525][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:13.529][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-07-23 21:29:13.533][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-07-23 21:29:13.537][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-07-23 21:29:13.540][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:13.542][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:13.544][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:13.548][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:13.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:13.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:13.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:13.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:13.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:13.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:13.575][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.578][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.593][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:13.595][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:13.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.599][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.602][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:13.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:13.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.609][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:13.612][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:13.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.615][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:13.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.625][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:13.627][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:13.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.631][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:13.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:13.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.639][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:13.640][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:13.641][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.642][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:13.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:13.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.651][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:13.653][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:13.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.656][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.658][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:13.659][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.661][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.663][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.665][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:13.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.673][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:13.675][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:13.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.678][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:13.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:13.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.685][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:13.687][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:13.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.689][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:13.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:13.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.698][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:13.700][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:13.701][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.703][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.705][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:13.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:13.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.713][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:13.715][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:13.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.718][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.721][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:13.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:13.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:13.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:13.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.734][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:13.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:13.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:13.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:13.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:13.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:13.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:13.821][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-07-23 21:29:13.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:13.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:13.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:13.837][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:13.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:13.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:13.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:13.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:13.851][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:13.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:13.854][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-07-23 21:29:13.856][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:13.858][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-07-23 21:29:13.861][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:13.863][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:13.864][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:13.866][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:13.868][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:13.869][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:13.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:13.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:13.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:13.887][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:13.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:13.891][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:13.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:13.894][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-07-23 21:29:13.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:13.900][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:13.903][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-07-23 21:29:14.321][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-07-23 21:29:14.714][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:14.717][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-07-23 21:29:14.722][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-07-23 21:29:14.726][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-07-23 21:29:14.728][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:14.729][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:14.731][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:14.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:14.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:14.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:14.742][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:14.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:14.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:14.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:14.749][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.751][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.754][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.760][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:14.761][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:14.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.764][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.765][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:14.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:14.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.770][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:14.772][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:14.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.774][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.776][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:14.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:14.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.781][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:14.782][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:14.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.784][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:14.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:14.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.791][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:14.792][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:14.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.794][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.796][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:14.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:14.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.801][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:14.802][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:14.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.804][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.806][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:14.807][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.809][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.810][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:14.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.815][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:14.817][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:14.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:14.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:14.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.825][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:14.826][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:14.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.829][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.830][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:14.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:14.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.835][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:14.836][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:14.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.838][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.839][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:14.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:14.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.844][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:14.845][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:14.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.847][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:14.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:14.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:14.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:14.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:14.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:14.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:14.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:14.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:14.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:14.921][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-07-23 21:29:14.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:14.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:14.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:14.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:14.942][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:14.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:14.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:14.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:14.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:14.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:14.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:14.960][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-07-23 21:29:14.962][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:14.964][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-07-23 21:29:14.966][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:14.967][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:14.968][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:14.969][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:14.970][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:14.971][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:14.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:14.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:14.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:14.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:14.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:14.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:14.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:14.992][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-07-23 21:29:14.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:14.999][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:15.001][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-07-23 21:29:15.428][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-07-23 21:29:15.829][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:15.832][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-07-23 21:29:15.836][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-07-23 21:29:15.839][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-07-23 21:29:15.840][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:15.842][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:15.843][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:15.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:15.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:15.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:15.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:15.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:15.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:15.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:15.857][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:15.858][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:15.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.860][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:15.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:15.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.866][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:15.867][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:15.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.869][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.870][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:15.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:15.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.875][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:15.876][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:15.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.878][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.879][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:15.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:15.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.884][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:15.885][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:15.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.887][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:15.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:15.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.893][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:15.894][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:15.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.896][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.898][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:15.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:15.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.902][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:15.903][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:15.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.905][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.907][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:15.908][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:15.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.910][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.911][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:15.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:15.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.923][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:15.929][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:15.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.932][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:15.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:15.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.937][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:15.938][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:15.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.940][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:15.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:15.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.945][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:15.946][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:15.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.948][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.950][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:15.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:15.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.953][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:15.954][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:15.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.961][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.963][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:15.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:15.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:15.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:15.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:15.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:15.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:15.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:15.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:15.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:15.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:15.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:15.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:15.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:15.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:15.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:15.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:15.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:15.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:15.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:15.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:16.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:16.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:16.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:16.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:16.010][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-07-23 21:29:16.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:16.025][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:16.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:16.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:16.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:16.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:16.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:16.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:16.038][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-07-23 21:29:16.039][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:16.042][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-07-23 21:29:16.043][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:16.045][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:16.046][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:16.047][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:16.048][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:16.049][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:16.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:16.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:16.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:16.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:16.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:16.065][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:16.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:16.067][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-07-23 21:29:16.071][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:16.072][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:16.074][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-07-23 21:29:16.472][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-07-23 21:29:16.880][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:16.883][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-07-23 21:29:16.886][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-07-23 21:29:16.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-07-23 21:29:16.890][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:16.891][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:16.893][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:16.896][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:16.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:16.898][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:16.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:16.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:16.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:16.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:16.908][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:16.909][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:16.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.911][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:16.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:16.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.916][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:16.917][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:16.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.919][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.920][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:16.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:16.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.924][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:16.926][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:16.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.927][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:16.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:16.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.952][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:16.953][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:16.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.955][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:16.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.960][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:16.961][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:16.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.964][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:16.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:16.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.969][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:16.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:16.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.973][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.974][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:16.975][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.977][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.978][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:16.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:16.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:16.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:16.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.984][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:16.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:16.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.989][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:16.990][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:16.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.992][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:16.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:16.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:16.997][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:16.998][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:16.999][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.000][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.001][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:17.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:17.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.005][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:17.006][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:17.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.008][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.009][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:17.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:17.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:17.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:17.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:17.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:17.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:17.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:17.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:17.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:17.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:17.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:17.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:17.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:17.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:17.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:17.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:17.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:17.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:17.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:17.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:17.049][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-07-23 21:29:17.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:17.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:17.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.054][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:17.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:17.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:17.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:17.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:17.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:17.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:17.078][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:17.081][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:17.082][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:17.084][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:17.684][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:18.230][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:18.237][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-07-23 21:29:18.246][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-07-23 21:29:18.254][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.400][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.422][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.547][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.622][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.624][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.679][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.705][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.710][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.792][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.974][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.978][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:18.982][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:18.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:18.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:18.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:18.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:18.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:18.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:18.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:18.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:18.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:18.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:19.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:19.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:19.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:19.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:19.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:19.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:19.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:19.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:19.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:19.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:19.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:19.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:19.037][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:19.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:19.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:19.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:19.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:19.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:19.083][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:19.084][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:19.086][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:19.493][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:19.907][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:19.913][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-07-23 21:29:19.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-07-23 21:29:19.931][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:19.937][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:19.939][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:19.941][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:20.342][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:20.764][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:20.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-07-23 21:29:20.771][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-07-23 21:29:20.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:20.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:20.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:20.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:20.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:20.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:20.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:20.786][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-07-23 21:29:20.787][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:20.789][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-07-23 21:29:20.790][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:20.791][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:20.793][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:20.794][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:20.795][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:20.796][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:20.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:20.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:20.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:20.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:20.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:20.809][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:20.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:20.811][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-07-23 21:29:20.814][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:20.816][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:20.817][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-07-23 21:29:21.233][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-07-23 21:29:21.669][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:21.672][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-07-23 21:29:21.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-07-23 21:29:21.678][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-07-23 21:29:21.680][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:21.681][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:21.682][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:21.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:21.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:21.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:21.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:21.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:21.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:21.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:21.696][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.698][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.700][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.705][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:21.706][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:21.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.708][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.709][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:21.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:21.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.714][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:21.715][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:21.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.717][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.718][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:21.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:21.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.723][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:21.724][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:21.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.726][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:21.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:21.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.731][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:21.732][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:21.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.734][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:21.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:21.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.740][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:21.741][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:21.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.743][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.745][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:21.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:21.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.749][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:21.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:21.751][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.752][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.753][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:21.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:21.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.757][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.759][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.766][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.774][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:21.775][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:21.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:21.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:21.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.820][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:21.822][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:21.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.824][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.825][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:21.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:21.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.830][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:21.831][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:21.832][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.833][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.835][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:21.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:21.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:21.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:21.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:21.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:21.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.848][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:21.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:21.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:21.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:21.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:21.881][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-07-23 21:29:21.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:21.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:21.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:21.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:21.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:21.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:21.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:21.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:21.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:21.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:21.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:21.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:21.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:21.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:21.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:21.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:21.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:21.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:21.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:21.930][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-07-23 21:29:21.931][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:21.933][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-07-23 21:29:21.934][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:21.935][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:21.936][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:21.937][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:21.938][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:21.940][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:21.943][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:21.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:21.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:21.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:21.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:21.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:21.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:21.954][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-07-23 21:29:21.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:21.958][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:21.959][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-07-23 21:29:22.347][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-07-23 21:29:22.767][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:22.770][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-07-23 21:29:22.773][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-07-23 21:29:22.775][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-07-23 21:29:22.777][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:22.778][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:22.779][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:22.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:22.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:22.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:22.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:22.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:22.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:22.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:22.792][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.793][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.795][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.809][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:22.810][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:22.811][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.812][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.813][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:22.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:22.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.817][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:22.818][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:22.819][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.819][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.821][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:22.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:22.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.825][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:22.826][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:22.826][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.827][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.828][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:22.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:22.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.832][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:22.833][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:22.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.835][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.836][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:22.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:22.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.840][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:22.841][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:22.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.843][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.844][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:22.845][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:22.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.847][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:22.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.852][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.853][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.854][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.859][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:22.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:22.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.862][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.863][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:22.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:22.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.867][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:22.868][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:22.869][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.870][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.871][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:22.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:22.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.875][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:22.876][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:22.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.877][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.879][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:22.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:22.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:22.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:22.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:22.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:22.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:22.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:22.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:22.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:22.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:22.920][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-07-23 21:29:22.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:22.949][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:22.952][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:22.953][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-23 21:29:22.955][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:22.956][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-23 21:29:22.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:22.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:22.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:22.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:22.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:22.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:22.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:22.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:22.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:22.987][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:22.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:22.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:22.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:22.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:22.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:22.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:22.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:22.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:22.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.023][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.068][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.072][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.114][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.121][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.167][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.208][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.214][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.228][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.270][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.291][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.348][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.373][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.407][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.430][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:23.434][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:23.435][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-07-23 21:29:23.436][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:23.438][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-07-23 21:29:23.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.449][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.463][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.483][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.505][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.510][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.521][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.533][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.540][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.575][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.590][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.592][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.596][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.605][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.662][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.677][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.684][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.729][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.748][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.805][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.811][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.844][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.876][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.880][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.935][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.956][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:23.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:23.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:23.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:23.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:23.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:23.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:23.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:23.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:23.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:23.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:23.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:24.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:24.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:24.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:24.044][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:24.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:24.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-23 21:29:24.069][biodb::testThat]
biodb.INFO [2024-07-23 21:29:24.070][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-23 21:29:24.072][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:24.074][biodb::testThat]
biodb.TRACE[2024-07-23 21:29:24.078][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-23 21:29:24.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-23 21:29:24.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:24.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:24.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:24.101][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:24.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:24.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:24.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:24.118][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:24.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:24.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:24.127][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:24.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:24.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:24.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:24.136][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:24.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:24.143][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:24.146][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:24.595][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:25.038][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:25.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-07-23 21:29:25.050][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-07-23 21:29:25.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:25.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:25.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:25.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:25.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:25.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:25.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:25.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:25.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:25.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:25.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:25.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:25.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:25.099][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:25.106][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:25.108][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:25.111][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:25.527][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:25.939][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:25.944][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-07-23 21:29:25.953][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-07-23 21:29:25.960][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:25.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:25.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:25.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:25.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:25.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:25.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:25.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:25.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:25.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:25.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:25.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:25.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:25.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:25.994][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:25.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:25.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:26.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:26.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:26.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:26.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:26.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:26.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:26.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:26.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:26.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:26.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:26.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:26.021][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-23 21:29:26.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:26.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:26.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:26.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:26.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:26.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:26.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:26.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.049][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.050][private$selectFields]
biodb.TRACE[2024-07-23 21:29:26.052][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:26.053][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:26.054][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.056][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.057][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.060][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.066][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.067][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.069][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.070][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.071][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.072][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.073][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:26.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.114][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-23 21:29:26.116][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:26.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:26.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:26.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:26.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:26.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:26.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:26.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.165][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.175][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.177][private$selectFields]
biodb.TRACE[2024-07-23 21:29:26.178][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:26.180][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:26.182][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.184][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.186][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.189][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.191][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.192][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.195][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.196][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.198][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.200][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.202][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.205][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.207][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:26.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.226][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-23 21:29:26.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:26.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:26.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:26.236][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:26.238][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:26.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:26.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:26.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.254][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.255][private$selectFields]
biodb.TRACE[2024-07-23 21:29:26.257][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:26.258][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:26.260][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.261][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.263][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.265][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.267][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.269][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.271][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.273][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.274][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:26.276][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.277][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.279][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.280][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:26.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:26.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.294][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-23 21:29:26.295][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-23 21:29:26.296][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-23 21:29:26.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:26.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:26.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:26.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:26.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:26.430][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:26.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:26.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:26.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:26.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:26.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:26.449][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:26.455][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:26.456][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:26.460][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:26.883][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:27.314][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:27.319][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-07-23 21:29:27.326][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-07-23 21:29:27.332][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:27.336][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:27.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:27.340][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:27.758][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:28.189][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:28.195][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-07-23 21:29:28.204][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-07-23 21:29:28.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:28.232][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:28.249][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.261][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.263][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:28.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:28.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:28.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:28.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:28.375][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-23 21:29:28.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.468][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:28.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.489][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.491][private$selectFields]
biodb.TRACE[2024-07-23 21:29:28.492][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:28.494][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:28.495][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.497][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.502][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.503][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.505][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.508][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.510][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.511][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.513][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.515][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.518][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.519][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:28.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.540][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-23 21:29:28.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.558][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.TRACE[2024-07-23 21:29:28.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.631][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.633][private$selectFields]
biodb.TRACE[2024-07-23 21:29:28.635][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:28.637][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:28.638][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.640][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.642][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.645][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.647][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.649][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.650][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.651][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.653][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.671][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.674][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.679][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.681][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:28.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.721][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-23 21:29:28.723][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:28.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.753][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.755][private$selectFields]
biodb.TRACE[2024-07-23 21:29:28.756][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:28.758][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:28.759][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.761][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.762][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.765][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.766][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.768][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.770][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.773][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:28.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.777][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.779][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.781][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:28.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:28.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.801][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-23 21:29:28.802][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-23 21:29:28.804][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-23 21:29:28.818][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:28.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:28.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-23 21:29:28.833][biodb::testThat]
biodb.INFO [2024-07-23 21:29:28.835][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-23 21:29:28.837][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:28.838][biodb::testThat]
biodb.TRACE[2024-07-23 21:29:28.844][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-23 21:29:28.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-23 21:29:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.864][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:28.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:28.905][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:28.910][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:28.913][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-23 21:29:28.915][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:28.919][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-23 21:29:28.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:28.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:28.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:28.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:28.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:28.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:28.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:28.963][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:28.969][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:28.973][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-23 21:29:28.975][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:28.978][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-23 21:29:28.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:28.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:28.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:28.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:28.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.000][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:29.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:29.085][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-23 21:29:29.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.104][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.121][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.122][private$selectFields]
biodb.TRACE[2024-07-23 21:29:29.124][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:29.126][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:29.127][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.129][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.131][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.134][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.136][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.138][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.141][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.143][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.145][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.148][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.151][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.153][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:29.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.178][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-23 21:29:29.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.200][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.TRACE[2024-07-23 21:29:29.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.211][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.219][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.220][private$selectFields]
biodb.TRACE[2024-07-23 21:29:29.222][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:29.224][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:29.225][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.227][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.232][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.234][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.235][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.239][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.240][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.242][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.244][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.246][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.248][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.249][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.250][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:29.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.273][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-23 21:29:29.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.309][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.310][private$selectFields]
biodb.TRACE[2024-07-23 21:29:29.312][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:29.313][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:29.315][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.316][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.318][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.321][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.323][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.345][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.348][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.350][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.353][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.355][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.357][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.359][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.361][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:29.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.387][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-23 21:29:29.389][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-23 21:29:29.391][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-23 21:29:29.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:29.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.464][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:29.471][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:29.477][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:29.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-23 21:29:29.482][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:29.484][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-23 21:29:29.489][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:29.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:29.497][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-23 21:29:29.500][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:29.502][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-23 21:29:29.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:29.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:29.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:29.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:29.623][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-23 21:29:29.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.642][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.663][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.665][private$selectFields]
biodb.TRACE[2024-07-23 21:29:29.682][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:29.685][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:29.688][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.690][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.692][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.696][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.698][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.700][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.704][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.706][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.707][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.709][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.711][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.713][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.714][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.716][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:29.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.726][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.737][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-23 21:29:29.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.763][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.764][private$selectFields]
biodb.TRACE[2024-07-23 21:29:29.765][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:29.766][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:29.767][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.768][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.769][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.772][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.773][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.778][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.779][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.781][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.783][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.787][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.789][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:29.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.812][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-23 21:29:29.813][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:29.814][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:29.815][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:29.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:29.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:29.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:29.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:29.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.838][private$selectFields]
biodb.TRACE[2024-07-23 21:29:29.840][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:29.842][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:29.843][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.846][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.848][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.850][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.851][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.854][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.856][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.858][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:29.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.860][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.863][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.865][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:29.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:29.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.890][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-23 21:29:29.891][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-23 21:29:29.892][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-23 21:29:29.910][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:29.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:29.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-23 21:29:29.925][biodb::testThat]
biodb.INFO [2024-07-23 21:29:29.928][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-23 21:29:29.930][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:29.932][biodb::testThat]
biodb.TRACE[2024-07-23 21:29:29.936][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-23 21:29:29.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-23 21:29:29.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.942][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.980][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:29.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:29.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:29.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.014][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:30.026][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:30.031][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:30.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-07-23 21:29:30.035][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:30.037][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-07-23 21:29:30.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.055][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.083][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:30.089][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:30.092][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-07-23 21:29:30.095][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:30.098][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-07-23 21:29:30.102][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:30.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.184][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-23 21:29:30.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.187][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.225][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.227][private$selectFields]
biodb.TRACE[2024-07-23 21:29:30.229][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:30.230][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:30.232][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.233][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.234][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.235][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.236][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.239][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.241][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.245][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.248][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.250][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.252][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.255][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.257][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:30.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.282][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-07-23 21:29:30.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.322][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.357][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.359][private$selectFields]
biodb.TRACE[2024-07-23 21:29:30.361][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:30.362][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:30.364][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.366][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.367][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.371][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.373][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.375][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.378][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.380][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.383][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.385][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.387][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.390][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.393][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:30.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.420][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-23 21:29:30.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.467][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.469][private$selectFields]
biodb.TRACE[2024-07-23 21:29:30.470][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:30.472][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:30.473][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.476][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.477][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.480][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.482][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.484][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.486][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.488][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.490][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.492][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.496][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.500][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.501][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:30.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.524][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-07-23 21:29:30.526][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-23 21:29:30.528][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-23 21:29:30.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.588][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.609][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.613][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:30.621][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:30.626][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:30.628][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-07-23 21:29:30.630][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:30.632][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-07-23 21:29:30.638][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:30.644][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:30.646][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-07-23 21:29:30.649][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:30.652][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-07-23 21:29:30.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:30.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:30.796][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-23 21:29:30.799][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.810][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.814][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.824][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.825][private$selectFields]
biodb.TRACE[2024-07-23 21:29:30.827][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:30.828][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:30.830][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.831][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.836][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.839][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.842][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.843][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.844][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.845][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.847][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.850][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.851][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:30.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.873][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-07-23 21:29:30.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.885][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.886][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.899][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.900][private$selectFields]
biodb.TRACE[2024-07-23 21:29:30.901][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:30.902][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:30.904][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.905][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.907][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.910][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.914][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.917][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.919][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.920][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:30.922][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.924][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.927][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.929][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:30.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.962][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-07-23 21:29:30.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:30.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:30.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:30.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:30.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:30.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:30.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:30.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:30.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:30.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:30.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:31.008][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:31.010][private$selectFields]
biodb.TRACE[2024-07-23 21:29:31.012][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-23 21:29:31.014][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-23 21:29:31.016][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:31.018][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.020][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.023][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:31.025][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.027][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.031][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:31.033][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:31.035][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-07-23 21:29:31.037][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.040][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.043][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:31.044][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-07-23 21:29:31.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:31.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:31.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:31.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:31.067][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-07-23 21:29:31.068][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-23 21:29:31.070][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-23 21:29:31.108][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:31.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-23 21:29:31.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:31.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-23 21:29:31.123][biodb::testThat]
biodb.INFO [2024-07-23 21:29:31.125][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-07-23 21:29:31.127][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:31.129][biodb::testThat]
biodb.DEBUG[2024-07-23 21:29:31.132][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-23 21:29:31.134][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:31.138][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-23 21:29:31.140][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:31.142][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:31.143][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:31.144][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:31.145][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:31.147][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:31.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:31.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:31.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:31.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:31.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:31.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:31.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:31.165][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-07-23 21:29:31.169][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:31.171][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:31.174][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-07-23 21:29:31.605][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-07-23 21:29:32.029][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:32.032][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-07-23 21:29:32.038][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-07-23 21:29:32.044][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-07-23 21:29:32.046][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:32.049][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:32.051][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:32.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:32.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:32.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:32.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:32.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:32.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:32.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:32.076][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.078][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.082][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.090][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:32.091][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:32.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.094][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.097][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:32.099][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:32.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.103][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.106][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:32.108][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:32.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.111][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.113][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:32.115][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:32.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.118][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.120][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:32.122][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:32.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.125][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.128][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:32.147][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:32.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.150][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.153][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:32.155][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:32.157][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.159][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.161][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:32.163][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:32.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.166][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.167][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:32.168][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:32.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.171][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.173][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:32.175][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:32.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.179][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:32.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:32.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:32.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:32.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.199][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:32.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:32.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:32.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:32.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:32.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:32.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:32.232][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-07-23 21:29:32.233][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-23 21:29:32.247][biodb::testThat]
biodb.INFO [2024-07-23 21:29:32.250][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-23 21:29:32.252][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:32.254][biodb::testThat]
biodb.DEBUG[2024-07-23 21:29:32.268][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-07-23 21:29:32.271][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-07-23 21:29:32.274][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-07-23 21:29:32.278][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-07-23 21:29:32.281][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-07-23 21:29:32.284][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:32.287][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:32.289][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:32.292][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:32.294][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:32.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:32.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:32.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:32.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:32.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:32.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:32.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:32.321][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-07-23 21:29:32.325][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:32.326][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:32.328][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-07-23 21:29:32.738][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-07-23 21:29:33.162][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:33.166][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-07-23 21:29:33.173][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-07-23 21:29:33.176][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:33.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:33.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:33.190][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:33.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:33.194][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:33.196][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:33.198][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-07-23 21:29:33.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:33.206][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:33.209][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-07-23 21:29:33.641][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-07-23 21:29:34.061][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:34.066][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-07-23 21:29:34.077][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-07-23 21:29:34.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:34.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:34.083][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:34.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:34.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:34.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:34.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:34.103][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-07-23 21:29:34.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:34.113][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:34.117][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-07-23 21:29:34.535][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-07-23 21:29:34.950][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:34.955][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-07-23 21:29:34.997][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-07-23 21:29:35.004][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-07-23 21:29:35.007][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:35.010][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-07-23 21:29:35.013][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:35.016][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:35.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:35.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:35.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:35.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:35.035][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:35.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:35.042][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.043][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.045][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.053][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:35.055][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:35.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.058][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.061][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:35.062][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:35.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.066][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:35.067][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:35.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.069][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.071][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.073][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.075][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.076][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.078][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.079][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.081][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.082][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:35.083][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:35.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.085][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.087][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.089][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.091][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.093][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:35.094][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:35.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.096][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.098][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:35.099][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:35.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.102][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.104][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:35.106][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:35.107][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:35.160][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:35.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:35.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:35.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:35.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:35.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:35.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:35.181][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.183][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.185][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.190][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:35.192][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:35.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.196][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.198][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:35.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:35.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.206][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:35.207][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:35.209][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.211][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:35.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:35.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.236][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:35.239][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:35.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.243][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:35.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:35.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.252][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.253][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.256][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.266][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.268][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.271][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.274][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.281][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:35.283][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:35.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.287][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.289][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:35.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:35.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.332][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.336][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.340][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.350][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:35.351][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:35.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.354][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.356][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:35.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:35.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.362][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:35.364][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:35.366][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.368][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.371][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:35.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:35.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.378][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:35.379][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:35.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.382][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.385][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:35.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:35.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:35.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:35.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:35.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:35.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:35.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:35.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:35.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:35.461][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.464][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.468][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.478][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:35.480][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:35.482][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.484][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.486][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:35.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:35.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.494][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:35.496][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:35.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.499][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.502][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:35.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:35.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.510][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:35.512][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:35.514][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.516][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:35.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:35.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.526][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.528][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.531][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:35.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.540][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.542][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.546][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.548][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:35.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.556][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:35.558][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:35.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.561][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.564][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:35.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:35.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.571][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.572][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.574][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:35.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.582][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:35.584][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:35.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.587][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:35.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:35.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.597][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:35.599][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:35.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.601][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.602][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:35.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:35.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:35.611][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:35.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.614][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:35.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:35.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:35.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:35.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:35.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:35.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:35.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:35.714][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-07-23 21:29:35.715][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-23 21:29:35.717][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-07-23 21:29:35.738][biodb::testThat]
biodb.INFO [2024-07-23 21:29:35.741][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-07-23 21:29:35.742][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:35.744][biodb::testThat]
biodb.INFO [2024-07-23 21:29:35.783][biodb::testThat]
biodb.INFO [2024-07-23 21:29:35.784][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-07-23 21:29:35.785][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:35.786][biodb::testThat]
biodb.INFO [2024-07-23 21:29:35.798][biodb::testThat]
biodb.INFO [2024-07-23 21:29:35.800][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-07-23 21:29:35.802][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:35.803][biodb::testThat]
biodb.DEBUG[2024-07-23 21:29:35.806][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:35.811][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:35.813][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:35.815][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:36.314][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:36.869][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:36.871][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-07-23 21:29:36.878][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-07-23 21:29:36.899][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:36.901][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:36.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:36.904][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:36.905][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:36.906][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:36.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:36.908][ef$get] fields variable is a list.
biodb.INFO [2024-07-23 21:29:36.909][biodb::testThat]
biodb.INFO [2024-07-23 21:29:36.910][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-23 21:29:36.911][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:36.912][biodb::testThat]
biodb.ERROR[2024-07-23 21:29:36.951][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-23 21:29:36.985][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-23 21:29:37.011][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-23 21:29:37.014][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-23 21:29:37.017][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-23 21:29:37.019][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-23 21:29:37.020][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:37.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:37.023][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.027][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-23 21:29:37.047][biodb::testContext]
biodb.INFO [2024-07-23 21:29:37.049][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:29:37.051][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-07-23 21:29:37.053][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:29:37.055][biodb::testContext]
biodb.INFO [2024-07-23 21:29:37.058][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:29:37.062][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-23 21:29:37.069][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:37.072][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-23 21:29:37.074][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-23 21:29:37.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.082][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-23 21:29:37.085][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-23 21:29:37.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.091][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-23 21:29:37.092][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-23 21:29:37.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.098][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-23 21:29:37.100][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-23 21:29:37.101][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-23 21:29:37.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.108][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-23 21:29:37.109][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-23 21:29:37.111][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-23 21:29:37.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.117][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-23 21:29:37.119][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-23 21:29:37.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.125][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-23 21:29:37.126][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-23 21:29:37.128][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-23 21:29:37.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.134][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-23 21:29:37.136][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-23 21:29:37.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.142][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-23 21:29:37.144][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-23 21:29:37.146][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-23 21:29:37.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.153][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:29:37.155][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-23 21:29:37.156][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-23 21:29:37.158][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-23 21:29:37.160][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-23 21:29:37.162][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-23 21:29:37.163][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.167][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-23 21:29:37.169][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-23 21:29:37.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.175][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-23 21:29:37.177][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-23 21:29:37.179][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.183][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-23 21:29:37.185][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-23 21:29:37.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.192][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-23 21:29:37.194][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-23 21:29:37.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.200][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-23 21:29:37.202][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-23 21:29:37.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.207][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:29:37.208][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-23 21:29:37.211][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-23 21:29:37.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.215][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-23 21:29:37.216][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-23 21:29:37.218][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-23 21:29:37.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.224][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-23 21:29:37.227][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.273][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-23 21:29:37.275][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.276][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:37.277][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.278][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.279][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.281][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.282][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:29:37.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:37.285][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.287][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-23 21:29:37.288][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:37.290][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.292][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:37.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:37.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:37.293][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:29:37.293][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:29:37.295][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:37.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.300][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:37.302][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.303][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.305][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.306][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.308][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:37.310][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:37.311][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.313][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.315][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-23 21:29:37.318][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.320][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:29:37.323][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.324][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:37.325][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.326][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.327][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.329][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.330][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:29:37.332][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:37.334][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.335][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-23 21:29:37.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:37.339][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.340][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.342][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:37.342][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:37.342][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:37.342][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:29:37.342][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:29:37.344][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:37.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.349][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:37.351][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.353][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.355][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.357][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.359][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:37.360][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:37.361][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.362][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.364][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-23 21:29:37.366][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.367][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-23 21:29:37.368][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.369][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:37.370][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.372][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.373][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.375][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.377][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:29:37.378][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:37.379][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.381][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-23 21:29:37.382][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:37.384][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.386][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.388][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.389][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:37.391][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.393][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.394][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:37.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.399][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.401][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.402][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:37.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:37.405][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.407][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.409][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-23 21:29:37.412][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.414][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:29:37.416][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.418][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:37.419][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.421][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.422][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.423][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.424][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:29:37.425][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:37.426][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.427][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-23 21:29:37.428][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:37.429][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.430][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:37.431][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.432][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:37.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.437][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:37.439][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:37.440][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:37.441][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:37.443][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.444][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:37.445][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:37.446][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:37.448][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:37.450][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:37.452][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.479][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.DEBUG[2024-07-23 21:29:37.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.810][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[2024-07-23 21:29:37.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.821][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[2024-07-23 21:29:37.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.860][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[2024-07-23 21:29:37.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:37.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:37.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:37.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:37.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:37.869][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-23 21:29:37.872][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-23 21:29:37.874][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-23 21:29:37.877][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-23 21:29:37.879][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:29:37.881][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-23 21:29:37.882][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-23 21:29:37.883][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-23 21:29:37.885][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-23 21:29:37.886][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-23 21:29:37.888][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:29:37.890][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-23 21:29:37.892][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-23 21:29:37.895][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-23 21:29:37.897][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-23 21:29:37.899][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-23 21:29:37.901][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-23 21:29:37.903][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-23 21:29:37.906][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:29:37.908][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-23 21:29:37.910][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-23 21:29:37.913][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-23 21:29:37.915][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-23 21:29:37.918][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-23 21:29:37.920][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-23 21:29:37.923][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-23 21:29:37.926][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-23 21:29:37.929][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-23 21:29:37.931][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-23 21:29:37.933][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-23 21:29:37.935][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-23 21:29:37.937][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-23 21:29:37.938][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-23 21:29:37.939][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-23 21:29:37.941][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-23 21:29:37.943][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-23 21:29:37.946][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-23 21:29:37.948][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-23 21:29:37.950][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-23 21:29:37.953][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-23 21:29:37.956][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-23 21:29:37.958][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-23 21:29:37.961][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-23 21:29:37.964][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-23 21:29:37.966][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-23 21:29:37.969][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-23 21:29:37.971][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-23 21:29:37.974][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-23 21:29:37.977][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-23 21:29:37.979][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-23 21:29:37.982][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-23 21:29:37.985][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-23 21:29:37.986][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-23 21:29:37.988][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-23 21:29:37.991][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-23 21:29:37.994][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-23 21:29:37.997][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-23 21:29:37.999][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-23 21:29:38.002][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-23 21:29:38.005][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-23 21:29:38.008][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-23 21:29:38.010][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-23 21:29:38.013][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-23 21:29:38.016][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-23 21:29:38.018][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-23 21:29:38.021][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-23 21:29:38.024][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:29:38.027][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:29:38.029][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-23 21:29:38.031][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-23 21:29:38.033][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-23 21:29:38.035][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-23 21:29:38.037][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-23 21:29:38.038][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-23 21:29:38.040][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-23 21:29:38.043][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-23 21:29:38.045][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-23 21:29:38.046][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-23 21:29:38.048][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-23 21:29:38.050][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-23 21:29:38.061][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-23 21:29:38.064][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-23 21:29:38.067][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-23 21:29:38.070][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-23 21:29:38.072][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:29:38.073][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:38.074][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.076][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.154][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.DEBUG[2024-07-23 21:29:38.155][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.173][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[2024-07-23 21:29:38.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:38.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:38.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:38.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:38.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:38.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:38.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:38.255][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[2024-07-23 21:29:38.259][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-23 21:29:38.263][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-23 21:29:38.267][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:38.269][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-23 21:29:38.271][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:38.273][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:38.275][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:38.278][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:38.279][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:38.281][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-23 21:29:38.282][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-23 21:29:38.283][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:38.285][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:38.286][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-23 21:29:38.287][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-23 21:29:38.289][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-23 21:29:38.291][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:38.293][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:38.293][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:38.293][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:38.295][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-23 21:29:38.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:38.299][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:38.301][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:38.303][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:38.305][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:38.307][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:38.309][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:38.309][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-23 21:29:38.311][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:38.313][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:38.315][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:38.317][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-23 21:29:38.317][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-23 21:29:38.319][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:29:38.322][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:29:38.326][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-23 21:29:38.329][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:29:38.332][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:29:38.336][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:29:38.343][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-23 21:29:38.346][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-23 21:29:38.349][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-23 21:29:38.352][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-23 21:29:38.371][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:29:38.373][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:29:38.375][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-23 21:29:38.376][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-23 21:29:38.379][biodb::testThat]
biodb.INFO [2024-07-23 21:29:38.380][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-07-23 21:29:38.381][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:38.382][biodb::testThat]
biodb.DEBUG[2024-07-23 21:29:38.390][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-23 21:29:38.397][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:38.399][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:38.402][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-07-23 21:29:38.830][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-07-23 21:29:39.416][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:39.421][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-07-23 21:29:39.458][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-07-23 21:29:39.465][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:39.470][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:39.471][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:39.474][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:39.895][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:40.322][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:40.325][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-07-23 21:29:40.332][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-07-23 21:29:40.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:40.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:40.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:40.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:40.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:40.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:40.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:40.356][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:40.361][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:40.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:40.365][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:40.779][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:41.196][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:41.201][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-07-23 21:29:41.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-07-23 21:29:41.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:41.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:41.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:41.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:41.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:41.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:41.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:41.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:41.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:41.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:41.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:41.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:41.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:41.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:41.283][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:41.286][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:41.287][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-23 21:29:41.289][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:41.292][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-23 21:29:41.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:41.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:41.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:41.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:41.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:41.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:41.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:41.313][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:41.319][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:41.321][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-23 21:29:41.323][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:41.324][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-23 21:29:41.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:41.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:41.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:41.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:41.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:41.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:41.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:41.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:41.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:41.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:41.366][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:41.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:41.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:41.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:41.376][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:41.380][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:41.383][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-07-23 21:29:41.385][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:41.388][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-07-23 21:29:41.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:41.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:41.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:41.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:41.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:41.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:41.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:41.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:41.411][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:41.413][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-07-23 21:29:41.414][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:41.416][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-07-23 21:29:41.418][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:41.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:41.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:41.427][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:41.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:41.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:41.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:41.435][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:41.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:41.443][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:41.447][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:41.892][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:42.332][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:42.340][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-07-23 21:29:42.349][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-07-23 21:29:42.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:42.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:42.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:42.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:42.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:42.374][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:42.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-23 21:29:42.388][biodb::testThat]
biodb.INFO [2024-07-23 21:29:42.391][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-07-23 21:29:42.393][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:42.394][biodb::testThat]
biodb.DEBUG[2024-07-23 21:29:42.401][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:42.409][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:42.411][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:42.416][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:42.828][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:43.251][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:43.254][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-07-23 21:29:43.258][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-07-23 21:29:43.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:43.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:43.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:43.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:43.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:43.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:43.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:43.278][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:43.283][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:43.285][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:43.289][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:43.717][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:44.154][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:44.159][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-07-23 21:29:44.167][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-07-23 21:29:44.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:44.173][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.190][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.INFO [2024-07-23 21:29:44.201][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-23 21:29:44.204][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-23 21:29:44.207][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-23 21:29:44.209][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-23 21:29:44.211][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.215][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.219][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-23 21:29:44.229][biodb::testContext]
biodb.INFO [2024-07-23 21:29:44.231][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:29:44.233][biodb::testContext] Test context - Test web services
biodb.INFO [2024-07-23 21:29:44.235][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:29:44.237][biodb::testContext]
biodb.INFO [2024-07-23 21:29:44.241][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:29:44.245][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-23 21:29:44.252][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:44.254][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-23 21:29:44.256][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-23 21:29:44.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.262][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-23 21:29:44.304][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-23 21:29:44.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.312][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-23 21:29:44.314][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-23 21:29:44.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.321][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-23 21:29:44.322][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-23 21:29:44.324][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-23 21:29:44.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.330][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-23 21:29:44.332][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-23 21:29:44.333][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-23 21:29:44.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.339][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-23 21:29:44.341][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-23 21:29:44.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.347][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-23 21:29:44.349][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-23 21:29:44.350][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-23 21:29:44.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.356][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-23 21:29:44.357][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-23 21:29:44.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.363][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-23 21:29:44.364][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-23 21:29:44.366][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-23 21:29:44.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.372][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:29:44.374][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-23 21:29:44.375][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-23 21:29:44.377][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-23 21:29:44.379][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-23 21:29:44.380][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-23 21:29:44.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.386][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-23 21:29:44.387][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-23 21:29:44.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.393][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-23 21:29:44.394][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-23 21:29:44.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.399][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-23 21:29:44.401][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-23 21:29:44.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.406][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-23 21:29:44.407][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-23 21:29:44.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.412][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-23 21:29:44.414][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-23 21:29:44.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.419][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:29:44.421][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-23 21:29:44.425][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-23 21:29:44.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.431][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-23 21:29:44.432][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-23 21:29:44.434][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-23 21:29:44.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.439][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-23 21:29:44.442][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.444][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-23 21:29:44.446][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.447][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:44.449][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.450][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.452][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.453][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.454][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:29:44.456][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:44.457][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.459][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-23 21:29:44.460][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:44.462][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.464][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.465][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:44.465][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:44.465][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:44.465][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:29:44.465][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:29:44.467][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:44.468][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.470][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.471][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:44.472][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.474][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.475][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.476][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.478][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:44.479][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:44.481][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.482][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.484][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-23 21:29:44.487][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.488][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:29:44.490][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.491][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:44.493][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.494][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.495][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.497][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.498][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:29:44.500][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:44.501][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.502][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-23 21:29:44.504][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:44.505][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.507][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.508][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:44.508][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:44.508][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:44.508][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:29:44.508][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:29:44.509][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:44.511][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.512][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.513][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:44.514][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.515][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.518][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.519][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:44.520][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:44.521][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.522][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.524][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-23 21:29:44.526][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.528][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-23 21:29:44.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.530][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:44.531][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.533][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.534][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.535][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.537][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:29:44.538][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:44.540][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.541][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-23 21:29:44.542][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:44.544][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.545][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.546][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.548][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:44.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.559][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:44.561][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.563][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.565][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.566][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:44.567][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:44.568][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.570][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.571][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-23 21:29:44.574][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.575][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:29:44.577][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.578][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:44.579][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.581][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.582][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.584][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.585][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:29:44.586][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:44.588][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.589][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-23 21:29:44.591][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:44.592][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.593][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.595][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.596][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:44.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.599][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.600][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:44.601][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.602][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.603][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.604][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.605][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:44.605][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:44.606][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.607][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:44.608][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:44.609][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.627][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.647][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.655][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[2024-07-23 21:29:44.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.665][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.667][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.672][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.680][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-23 21:29:44.682][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-23 21:29:44.683][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-23 21:29:44.685][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-23 21:29:44.686][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:29:44.687][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-23 21:29:44.689][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-23 21:29:44.690][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-23 21:29:44.691][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-23 21:29:44.693][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-23 21:29:44.694][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:29:44.695][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-23 21:29:44.702][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-23 21:29:44.704][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-23 21:29:44.705][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-23 21:29:44.707][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-23 21:29:44.708][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-23 21:29:44.710][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-23 21:29:44.711][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:29:44.713][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-23 21:29:44.714][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-23 21:29:44.716][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-23 21:29:44.717][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-23 21:29:44.719][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-23 21:29:44.720][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-23 21:29:44.722][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-23 21:29:44.723][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-23 21:29:44.725][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-23 21:29:44.726][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-23 21:29:44.728][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-23 21:29:44.729][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-23 21:29:44.731][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-23 21:29:44.732][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-23 21:29:44.752][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-23 21:29:44.754][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-23 21:29:44.755][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-23 21:29:44.757][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-23 21:29:44.758][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-23 21:29:44.760][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-23 21:29:44.761][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-23 21:29:44.763][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-23 21:29:44.764][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-23 21:29:44.766][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-23 21:29:44.767][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-23 21:29:44.768][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-23 21:29:44.770][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-23 21:29:44.771][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-23 21:29:44.773][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-23 21:29:44.774][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-23 21:29:44.776][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-23 21:29:44.777][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-23 21:29:44.779][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-23 21:29:44.780][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-23 21:29:44.782][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-23 21:29:44.783][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-23 21:29:44.784][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-23 21:29:44.786][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-23 21:29:44.787][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-23 21:29:44.789][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-23 21:29:44.790][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-23 21:29:44.792][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-23 21:29:44.793][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-23 21:29:44.794][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-23 21:29:44.796][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-23 21:29:44.797][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-23 21:29:44.799][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-23 21:29:44.800][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:29:44.801][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:29:44.803][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-23 21:29:44.804][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-23 21:29:44.806][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-23 21:29:44.807][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-23 21:29:44.809][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-23 21:29:44.810][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-23 21:29:44.812][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-23 21:29:44.813][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-23 21:29:44.814][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-23 21:29:44.816][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-23 21:29:44.817][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-23 21:29:44.819][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-23 21:29:44.820][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-23 21:29:44.822][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-23 21:29:44.823][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-23 21:29:44.825][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-23 21:29:44.826][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:29:44.827][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:44.828][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.830][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.837][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.DEBUG[2024-07-23 21:29:44.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.864][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.867][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[2024-07-23 21:29:44.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.873][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[2024-07-23 21:29:44.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.903][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[2024-07-23 21:29:44.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.909][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[2024-07-23 21:29:44.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:44.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:44.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:44.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:44.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:44.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:44.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:44.938][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-23 21:29:44.940][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-23 21:29:44.942][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.942][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.943][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.944][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:44.945][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.946][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.947][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.948][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-23 21:29:44.949][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-23 21:29:44.950][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:44.951][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.951][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-23 21:29:44.952][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-23 21:29:44.953][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-23 21:29:44.954][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:44.955][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:44.955][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:44.955][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:44.956][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-23 21:29:44.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.959][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:44.959][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:44.960][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:44.961][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:44.962][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:44.962][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-23 21:29:44.963][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:44.964][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:44.965][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:44.966][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-23 21:29:44.966][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-23 21:29:44.967][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:29:44.968][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:29:44.970][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-23 21:29:44.971][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:29:44.972][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:29:44.974][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:29:44.977][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-23 21:29:44.978][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-23 21:29:44.979][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-23 21:29:44.981][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-23 21:29:44.982][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:29:44.983][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:29:44.984][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-23 21:29:44.985][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-23 21:29:44.986][biodb::testThat]
biodb.INFO [2024-07-23 21:29:44.987][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-07-23 21:29:44.988][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:44.989][biodb::testThat]
biodb.DEBUG[2024-07-23 21:29:44.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-23 21:29:44.996][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:44.997][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-23 21:29:44.998][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:45.000][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-23 21:29:45.004][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:45.007][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:45.008][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:45.009][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-07-23 21:29:45.403][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-07-23 21:29:45.796][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:45.799][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-07-23 21:29:45.806][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-07-23 21:29:45.820][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-23 21:29:45.822][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-23 21:29:45.824][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-23 21:29:45.825][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-23 21:29:45.827][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:45.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:45.830][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:45.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:45.833][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-23 21:29:45.840][biodb::testContext]
biodb.INFO [2024-07-23 21:29:45.841][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:29:45.843][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-07-23 21:29:45.844][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-23 21:29:45.846][biodb::testContext]
biodb.INFO [2024-07-23 21:29:45.849][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:29:45.851][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-07-23 21:29:45.856][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:45.857][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-23 21:29:45.859][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-23 21:29:45.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.863][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-23 21:29:45.864][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-23 21:29:45.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.868][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-23 21:29:45.869][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-23 21:29:45.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.872][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[2024-07-23 21:29:45.873][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-23 21:29:45.874][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-23 21:29:45.875][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-23 21:29:45.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.878][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-23 21:29:45.879][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-23 21:29:45.880][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-23 21:29:45.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.884][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-23 21:29:45.885][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-23 21:29:45.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.893][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-23 21:29:45.899][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-23 21:29:45.900][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-23 21:29:45.901][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.903][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-23 21:29:45.904][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-23 21:29:45.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.908][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-23 21:29:45.909][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-23 21:29:45.910][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-23 21:29:45.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.913][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:29:45.914][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-23 21:29:45.915][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-23 21:29:45.916][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-23 21:29:45.917][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-23 21:29:45.918][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-23 21:29:45.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.921][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-23 21:29:45.922][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-23 21:29:45.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.925][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-23 21:29:45.926][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-23 21:29:45.927][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.930][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-23 21:29:45.931][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-23 21:29:45.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.934][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-23 21:29:45.935][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-23 21:29:45.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.938][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-23 21:29:45.939][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-23 21:29:45.940][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.942][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-23 21:29:45.943][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-23 21:29:45.946][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-23 21:29:45.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.949][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-23 21:29:45.950][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-23 21:29:45.951][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-23 21:29:45.952][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:45.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:45.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:45.955][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-23 21:29:45.956][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:45.957][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-23 21:29:45.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:45.960][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.961][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:45.962][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:45.963][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:45.964][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:29:45.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:45.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.967][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-23 21:29:45.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:45.969][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:45.969][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.970][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:45.970][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:45.970][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:45.970][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:29:45.970][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:29:45.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:45.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:45.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:45.974][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:45.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:45.976][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:45.976][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:45.977][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:45.978][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:45.979][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:45.980][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:45.981][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:45.982][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-23 21:29:45.983][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:45.984][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:29:45.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:45.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.988][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:45.989][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:45.990][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:45.991][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:29:45.992][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:45.993][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.994][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-23 21:29:45.994][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:45.995][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:45.996][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:45.997][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:45.997][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:45.997][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:45.997][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-23 21:29:45.997][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-23 21:29:45.998][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:45.999][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.000][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:46.002][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.003][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.004][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.004][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:46.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:46.007][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.008][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.009][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-23 21:29:46.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-23 21:29:46.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:46.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.018][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-23 21:29:46.019][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:46.020][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.021][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-23 21:29:46.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:46.023][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.024][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.025][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:46.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:46.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.032][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.033][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.034][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:46.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:46.036][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.037][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.038][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-23 21:29:46.040][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.041][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-23 21:29:46.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.043][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:46.044][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.045][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.046][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.048][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-23 21:29:46.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:46.050][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.051][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-23 21:29:46.057][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:46.058][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.059][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.060][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.060][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-23 21:29:46.061][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.063][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:46.064][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.066][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.067][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.067][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:46.068][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:46.069][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.070][self$setPropertyValue]
biodb.DEBUG[2024-07-23 21:29:46.071][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:46.072][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.081][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.DEBUG[2024-07-23 21:29:46.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.096][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.102][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.110][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.143][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-23 21:29:46.144][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-23 21:29:46.146][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-23 21:29:46.147][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-23 21:29:46.148][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:29:46.149][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-23 21:29:46.151][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-23 21:29:46.152][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-23 21:29:46.153][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-23 21:29:46.155][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-23 21:29:46.156][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:29:46.157][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-23 21:29:46.158][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-23 21:29:46.160][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-23 21:29:46.161][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-23 21:29:46.162][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-23 21:29:46.163][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-23 21:29:46.165][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-23 21:29:46.166][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:29:46.167][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-23 21:29:46.169][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-23 21:29:46.170][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-23 21:29:46.171][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-23 21:29:46.173][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-23 21:29:46.174][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-23 21:29:46.175][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-23 21:29:46.177][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-23 21:29:46.178][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-23 21:29:46.179][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-23 21:29:46.181][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-23 21:29:46.182][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-23 21:29:46.183][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-23 21:29:46.185][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-23 21:29:46.186][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-23 21:29:46.187][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-23 21:29:46.188][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-23 21:29:46.190][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-23 21:29:46.191][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-23 21:29:46.192][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-23 21:29:46.194][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-23 21:29:46.195][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-23 21:29:46.197][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-23 21:29:46.198][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-23 21:29:46.199][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-23 21:29:46.201][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-23 21:29:46.202][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-23 21:29:46.208][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-23 21:29:46.209][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-23 21:29:46.211][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-23 21:29:46.212][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-23 21:29:46.213][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-23 21:29:46.214][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-23 21:29:46.216][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-23 21:29:46.217][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-23 21:29:46.218][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-23 21:29:46.219][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-23 21:29:46.221][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-23 21:29:46.222][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-23 21:29:46.223][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-23 21:29:46.224][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-23 21:29:46.226][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-23 21:29:46.227][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-23 21:29:46.228][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-23 21:29:46.229][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-23 21:29:46.231][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-23 21:29:46.232][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-23 21:29:46.233][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:29:46.234][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:29:46.236][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-23 21:29:46.237][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-23 21:29:46.238][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-23 21:29:46.239][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-23 21:29:46.241][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-23 21:29:46.242][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-23 21:29:46.243][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-23 21:29:46.244][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-23 21:29:46.246][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-23 21:29:46.247][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-23 21:29:46.248][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-23 21:29:46.249][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-23 21:29:46.251][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-23 21:29:46.252][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-23 21:29:46.253][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-23 21:29:46.254][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-23 21:29:46.256][initialize] This is biodb version 1.13.0.
biodb.DEBUG[2024-07-23 21:29:46.257][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-23 21:29:46.258][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.259][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.260][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[2024-07-23 21:29:46.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.294][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.345][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-23 21:29:46.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.362][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-07-23 21:29:46.363][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-07-23 21:29:46.365][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.365][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.366][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.367][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-23 21:29:46.368][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.369][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.370][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.371][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-07-23 21:29:46.372][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-07-23 21:29:46.373][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-23 21:29:46.373][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.374][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-07-23 21:29:46.375][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-07-23 21:29:46.376][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-07-23 21:29:46.377][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-23 21:29:46.378][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-23 21:29:46.378][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-23 21:29:46.378][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-23 21:29:46.379][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-07-23 21:29:46.380][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.381][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.382][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-23 21:29:46.382][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-23 21:29:46.383][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-23 21:29:46.384][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-23 21:29:46.385][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:46.385][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-07-23 21:29:46.386][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-23 21:29:46.387][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-23 21:29:46.387][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-23 21:29:46.388][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-07-23 21:29:46.388][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-07-23 21:29:46.390][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-23 21:29:46.391][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-23 21:29:46.392][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-07-23 21:29:46.394][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-23 21:29:46.395][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-23 21:29:46.396][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-23 21:29:46.399][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-07-23 21:29:46.400][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-07-23 21:29:46.401][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-07-23 21:29:46.403][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-07-23 21:29:46.404][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:29:46.405][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-07-23 21:29:46.406][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-07-23 21:29:46.407][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-07-23 21:29:46.408][biodb::testThat]
biodb.INFO [2024-07-23 21:29:46.409][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-07-23 21:29:46.410][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-23 21:29:46.410][biodb::testThat]
biodb.DEBUG[2024-07-23 21:29:46.413][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-07-23 21:29:46.416][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:46.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-07-23 21:29:46.419][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:46.420][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-07-23 21:29:46.423][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-07-23 21:29:46.426][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-23 21:29:46.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-07-23 21:29:46.428][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-23 21:29:46.429][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-07-23 21:29:46.444][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-07-23 21:29:46.445][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-23 21:29:46.447][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-07-23 21:29:46.448][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-23 21:29:46.449][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-23 21:29:46.450][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-07-23 21:29:46.451][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-07-23 21:29:46.452][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-23 21:29:46.452][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-23 21:29:46.455][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:46.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:46.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:46.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:46.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:46.462][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:46.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-23 21:29:46.464][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-07-23 21:29:46.467][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-23 21:29:46.468][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-23 21:29:46.469][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-07-23 21:29:46.859][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-07-23 21:29:48.009][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-23 21:29:48.012][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-07-23 21:29:48.015][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-07-23 21:29:48.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-07-23 21:29:48.019][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-23 21:29:48.021][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-07-23 21:29:48.022][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-07-23 21:29:48.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-23 21:29:48.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:48.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:48.030][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:48.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:48.032][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:48.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-23 21:29:48.037][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.040][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.046][ef$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:48.047][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:48.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.058][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.059][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-07-23 21:29:48.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-07-23 21:29:48.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.063][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:48.064][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:48.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.065][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-23 21:29:48.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-23 21:29:48.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.071][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-07-23 21:29:48.072][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-07-23 21:29:48.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.073][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.075][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-07-23 21:29:48.076][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-07-23 21:29:48.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.077][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.079][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:48.080][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:48.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.081][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.083][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:48.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-23 21:29:48.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.086][ef$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:48.087][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:48.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.089][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.090][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-07-23 21:29:48.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-23 21:29:48.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:48.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:48.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.097][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:48.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-23 21:29:48.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.102][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:48.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:48.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.104][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.106][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-23 21:29:48.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-23 21:29:48.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.110][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:48.111][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:48.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.112][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.114][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-07-23 21:29:48.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-07-23 21:29:48.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.117][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:48.118][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:48.119][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.120][ef$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.121][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-07-23 21:29:48.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-07-23 21:29:48.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:48.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:48.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:48.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:48.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-23 21:29:48.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-23 21:29:48.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-23 21:29:48.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-23 21:29:48.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-23 21:29:48.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-23 21:29:48.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-23 21:29:48.161][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-07-23 21:29:48.164][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-23 21:29:48.165][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-07-23 21:29:48.166][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-07-23 21:29:48.167][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-23 21:29:48.168][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-23 21:29:48.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-23 21:29:48.169][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-23 21:29:48.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-23 21:29:48.171][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-23 21:29:48.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
 28.339   1.152  61.523

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	1.018	0.067	1.989
ChebiEntry	0.153	0.005	0.159