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This page was generated on 2024-03-27 11:39:01 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4698
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4436
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4461
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4376
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 199/2264HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biodbChebi 1.9.0  (landing page)
Pierrick Roger
Snapshot Date: 2024-03-26 14:00:18 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/biodbChebi
git_branch: devel
git_last_commit: 6eb1625
git_last_commit_date: 2023-10-24 11:36:37 -0400 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for biodbChebi on lconway


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

raw results


Summary

Package: biodbChebi
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.9.0.tar.gz
StartedAt: 2024-03-26 19:08:40 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 19:10:53 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 132.8 seconds
RetCode: 0
Status:   OK  
CheckDir: biodbChebi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
ChebiConn 2.943  1.092   5.466
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK


Installation output

biodbChebi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘biodbChebi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biodbChebi)

Tests output

biodbChebi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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

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

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

> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-03-26 19:09:44.744][biodb::testContext]
biodb.INFO [2024-03-26 19:09:44.748][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:09:44.750][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-26 19:09:44.751][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:09:44.753][biodb::testContext]
biodb.INFO [2024-03-26 19:09:44.762][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:09:44.765][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-26 19:09:44.777][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:09:44.778][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-26 19:09:44.780][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-26 19:09:44.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.786][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-26 19:09:44.819][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-26 19:09:44.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.825][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-26 19:09:44.826][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-26 19:09:44.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.832][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-26 19:09:44.833][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-26 19:09:44.835][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-26 19:09:44.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.839][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.DEBUG[2024-03-26 19:09:44.841][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-26 19:09:44.842][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-26 19:09:44.843][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-26 19:09:44.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.848][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-26 19:09:44.850][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-26 19:09:44.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.855][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-26 19:09:44.856][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-26 19:09:44.858][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-26 19:09:44.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.863][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-26 19:09:44.864][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-26 19:09:44.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.883][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[2024-03-26 19:09:44.885][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-26 19:09:44.886][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-26 19:09:44.888][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-26 19:09:44.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.892][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:09:44.894][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-26 19:09:44.895][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-26 19:09:44.896][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-26 19:09:44.897][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-26 19:09:44.899][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-26 19:09:44.900][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.903][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[2024-03-26 19:09:44.904][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-26 19:09:44.906][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-26 19:09:44.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.911][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-26 19:09:44.912][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-26 19:09:44.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.917][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-26 19:09:44.918][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-26 19:09:44.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.923][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-26 19:09:44.924][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-26 19:09:44.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.929][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-26 19:09:44.931][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-26 19:09:44.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.936][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:09:44.937][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-26 19:09:44.962][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-26 19:09:44.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.966][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-26 19:09:44.968][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-26 19:09:44.969][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-26 19:09:44.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:44.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:44.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:44.978][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-26 19:09:45.031][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.053][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-26 19:09:45.055][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.057][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:09:45.058][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.060][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.062][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.063][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.065][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:09:45.066][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:09:45.067][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.069][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-26 19:09:45.070][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:09:45.071][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.073][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.074][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:09:45.074][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:09:45.074][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:09:45.074][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:09:45.074][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:09:45.076][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:09:45.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.080][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:09:45.081][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.082][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.083][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.085][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.086][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:09:45.087][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:09:45.089][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.090][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.092][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-26 19:09:45.094][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.096][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:09:45.098][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.099][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:09:45.100][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.102][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.104][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.105][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.106][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:09:45.108][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:09:45.110][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.111][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-26 19:09:45.112][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:09:45.114][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.115][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.116][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:09:45.116][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:09:45.116][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:09:45.116][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:09:45.116][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:09:45.118][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:09:45.119][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.120][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.121][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:09:45.123][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.125][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.126][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.127][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.129][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:09:45.130][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:09:45.131][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.132][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.134][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-26 19:09:45.137][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.138][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-26 19:09:45.140][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.141][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:09:45.143][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.144][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.145][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.147][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.148][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:09:45.149][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:09:45.151][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.152][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-26 19:09:45.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:09:45.155][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.156][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.158][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.159][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:09:45.160][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.161][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.162][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:09:45.164][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.165][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.166][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.167][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.169][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:09:45.170][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:09:45.171][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.173][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.175][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-26 19:09:45.177][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.178][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:09:45.179][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.181][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:09:45.182][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.183][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.184][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.186][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.187][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:09:45.188][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:09:45.190][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.191][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-26 19:09:45.193][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:09:45.194][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.196][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.198][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.207][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:09:45.208][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.209][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.211][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:09:45.212][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.213][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.215][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.217][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.218][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:09:45.219][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:09:45.221][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.222][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:09:45.226][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:09:45.228][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.269][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.271][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[2024-03-26 19:09:45.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.277][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[2024-03-26 19:09:45.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.284][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[2024-03-26 19:09:45.285][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.307][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.336][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[2024-03-26 19:09:45.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.354][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[2024-03-26 19:09:45.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.361][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[2024-03-26 19:09:45.363][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-26 19:09:45.370][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-26 19:09:45.372][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-26 19:09:45.374][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-26 19:09:45.376][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:09:45.378][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-26 19:09:45.380][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-26 19:09:45.382][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-26 19:09:45.384][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-26 19:09:45.386][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-26 19:09:45.388][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:09:45.390][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-26 19:09:45.392][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-26 19:09:45.394][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-26 19:09:45.396][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-26 19:09:45.398][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-26 19:09:45.400][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-26 19:09:45.402][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-26 19:09:45.404][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:09:45.407][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-26 19:09:45.408][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-26 19:09:45.410][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-26 19:09:45.412][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-26 19:09:45.414][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-26 19:09:45.416][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-26 19:09:45.418][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-26 19:09:45.420][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-26 19:09:45.422][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-26 19:09:45.424][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-26 19:09:45.426][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-26 19:09:45.428][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-26 19:09:45.430][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-26 19:09:45.432][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-26 19:09:45.434][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-26 19:09:45.436][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-26 19:09:45.438][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-26 19:09:45.440][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-26 19:09:45.442][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-26 19:09:45.444][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-26 19:09:45.446][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-26 19:09:45.447][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-26 19:09:45.450][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-26 19:09:45.452][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-26 19:09:45.454][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-26 19:09:45.457][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-26 19:09:45.458][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-26 19:09:45.461][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-26 19:09:45.462][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-26 19:09:45.465][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-26 19:09:45.467][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-26 19:09:45.469][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-26 19:09:45.470][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-26 19:09:45.472][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-26 19:09:45.474][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-26 19:09:45.476][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-26 19:09:45.478][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-26 19:09:45.480][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-26 19:09:45.482][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-26 19:09:45.484][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-26 19:09:45.486][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-26 19:09:45.487][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-26 19:09:45.490][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-26 19:09:45.492][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-26 19:09:45.494][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-26 19:09:45.496][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-26 19:09:45.498][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-26 19:09:45.500][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:09:45.503][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:09:45.504][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-26 19:09:45.506][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-26 19:09:45.508][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-26 19:09:45.510][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-26 19:09:45.512][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-26 19:09:45.514][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-26 19:09:45.517][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-26 19:09:45.519][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-26 19:09:45.520][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-26 19:09:45.522][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-26 19:09:45.524][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-26 19:09:45.525][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-26 19:09:45.535][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-26 19:09:45.537][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-26 19:09:45.539][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-26 19:09:45.547][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-26 19:09:45.549][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:09:45.554][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:09:45.556][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.558][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.592][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.600][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.DEBUG[2024-03-26 19:09:45.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.636][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.642][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[2024-03-26 19:09:45.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.680][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[2024-03-26 19:09:45.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:09:45.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:45.707][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-26 19:09:45.721][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-26 19:09:45.724][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.726][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.727][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.729][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:09:45.731][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.732][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.733][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.734][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-26 19:09:45.736][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-26 19:09:45.737][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:09:45.739][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.740][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-26 19:09:45.742][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-26 19:09:45.743][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-26 19:09:45.744][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-26 19:09:45.745][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:09:45.745][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:09:45.745][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:09:45.747][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-26 19:09:45.748][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.751][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:09:45.753][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:09:45.754][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:09:45.755][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:09:45.757][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:45.757][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-26 19:09:45.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:09:45.759][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:09:45.761][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-26 19:09:45.762][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-26 19:09:45.762][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-26 19:09:45.770][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:09:45.772][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:09:45.774][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-26 19:09:45.777][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:09:45.779][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:09:45.782][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:09:45.815][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-26 19:09:45.816][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-26 19:09:45.822][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-26 19:09:45.837][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-26 19:09:45.843][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:09:45.845][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:09:45.848][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-26 19:09:45.849][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-26 19:09:45.862][biodb::testThat]
biodb.INFO [2024-03-26 19:09:45.864][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2024-03-26 19:09:45.865][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:45.867][biodb::testThat]
biodb.TRACE[2024-03-26 19:09:45.888][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-03-26 19:09:45.891][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:45.895][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:45.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:45.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:45.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:45.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:45.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:45.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:45.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:45.942][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:45.944][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:45.946][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:45.948][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:45.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:45.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:45.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:45.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:45.969][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:45.970][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:45.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:45.972][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.010][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:46.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:46.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.017][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:46.018][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:46.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.021][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:46.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:46.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.029][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:46.030][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:46.031][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.033][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:46.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:46.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.040][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.041][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.044][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.050][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.052][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.054][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.056][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.061][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:46.062][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.064][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.065][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:46.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.070][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.071][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.072][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.073][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.080][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:46.081][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:46.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.083][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:46.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:46.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.090][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:46.091][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.093][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.095][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:46.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.101][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:46.102][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:46.104][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.105][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.107][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:46.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:46.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.113][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:46.228][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-03-26 19:09:46.231][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:46.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:46.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.236][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:46.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:46.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.276][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.300][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-26 19:09:46.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-26 19:09:46.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.305][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-26 19:09:46.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-26 19:09:46.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.311][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-26 19:09:46.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-26 19:09:46.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-26 19:09:46.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-26 19:09:46.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.513][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.514][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.516][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.517][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:46.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:46.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.559][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.560][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.563][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:46.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:46.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:46.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:46.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:46.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:46.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:46.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.601][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:46.602][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:46.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.604][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.606][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:46.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:46.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.626][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:46.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:46.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.632][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:46.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.638][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:46.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:46.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.644][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:46.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:46.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.648][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:46.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.676][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.695][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.697][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.699][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.700][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:46.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.737][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.739][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.742][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.743][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:46.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.763][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:46.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:46.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:46.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:46.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.775][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:46.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:46.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.781][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:46.782][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:46.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.785][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.786][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:46.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:46.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.806][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.811][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.817][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.822][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.823][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.826][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:46.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.846][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.853][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.859][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.864][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.866][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.868][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.869][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:46.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.887][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:46.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:46.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:46.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:46.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.898][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:46.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:46.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.905][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:46.906][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:46.908][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.909][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.911][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:46.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:46.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.930][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.948][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.950][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.951][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.952][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:46.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:46.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:46.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:46.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:46.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.001][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:47.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:47.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:47.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:47.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.011][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:47.013][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:47.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.015][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:47.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:47.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.036][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.040][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.050][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:47.052][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:47.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.054][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.064][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:47.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:47.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.068][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.078][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:47.079][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:47.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.082][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.091][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:47.092][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:47.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.095][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.105][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:47.107][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:47.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.110][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.119][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:47.121][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:47.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.123][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.133][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.134][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.136][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.137][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.147][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-03-26 19:09:47.148][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:47.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.151][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.160][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.162][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.165][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.174][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:47.175][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:47.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.178][ef$get] fields variable is a list.
biodb.INFO [2024-03-26 19:09:47.200][biodb::testThat]
biodb.INFO [2024-03-26 19:09:47.201][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-26 19:09:47.203][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:47.204][biodb::testThat]
biodb.DEBUG[2024-03-26 19:09:47.223][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-03-26 19:09:47.234][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:47.240][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-03-26 19:09:47.241][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:47.243][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-03-26 19:09:47.245][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:47.290][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:47.292][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:47.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:47.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:47.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:47.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:47.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:47.309][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:47.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:47.314][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.315][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.318][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.349][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:47.351][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:47.352][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.354][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.356][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:47.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:47.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.362][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:47.364][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:47.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.367][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.369][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:47.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:47.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.374][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:47.376][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:47.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.379][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:47.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:47.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.386][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:47.387][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:47.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.390][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.391][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:47.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:47.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.397][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:47.398][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:47.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.401][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.402][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:47.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:47.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.406][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:47.407][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:47.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.409][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:47.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:47.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.417][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.419][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.421][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.423][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.430][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.432][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.433][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.434][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.442][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:47.444][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:47.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.446][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.447][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:47.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:47.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.452][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:47.453][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:47.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.456][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.458][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:47.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:47.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:47.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:47.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:47.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:47.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:47.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:47.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.503][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:47.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:47.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:47.544][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-03-26 19:09:47.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-26 19:09:47.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-26 19:09:47.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.551][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-26 19:09:47.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-26 19:09:47.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-26 19:09:47.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-26 19:09:47.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-26 19:09:47.576][biodb::testThat]
biodb.INFO [2024-03-26 19:09:47.578][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-26 19:09:47.579][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:47.581][biodb::testThat]
biodb.TRACE[2024-03-26 19:09:47.585][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.587][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.590][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:47.592][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-03-26 19:09:47.638][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:47.661][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-03-26 19:09:47.669][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-26 19:09:47.699][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:47.722][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-26 19:09:47.725][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:47.727][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-26 19:09:47.761][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[2024-03-26 19:09:47.766][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:47.768][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:09:47.770][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:47.789][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-26 19:09:47.792][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-03-26 19:09:47.822][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.824][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:47.825][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.826][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.827][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:47.829][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:47.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.831][ef$get] fields variable is a list.
biodb.INFO [2024-03-26 19:09:47.844][biodb::testThat]
biodb.INFO [2024-03-26 19:09:47.845][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2024-03-26 19:09:47.847][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:47.848][biodb::testThat]
biodb.TRACE[2024-03-26 19:09:47.888][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.893][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:47.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:47.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:47.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:47.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:47.987][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[2024-03-26 19:09:47.992][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:47.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:09:47.996][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:47.998][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-03-26 19:09:48.030][biodb::testThat]
biodb.INFO [2024-03-26 19:09:48.031][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2024-03-26 19:09:48.033][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:48.034][biodb::testThat]
biodb.TRACE[2024-03-26 19:09:48.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:48.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:48.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:48.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:48.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.108][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.114][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.119][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-26 19:09:48.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-26 19:09:48.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.125][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-26 19:09:48.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-26 19:09:48.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:48.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:48.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:48.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:48.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.189][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:48.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:48.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.214][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-26 19:09:48.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.219][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-26 19:09:48.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-26 19:09:48.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:48.225][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-26 19:09:48.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-26 19:09:48.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:48.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-26 19:09:48.241][biodb::testThat]
biodb.INFO [2024-03-26 19:09:48.243][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-26 19:09:48.244][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:48.246][biodb::testThat]
biodb.INFO [2024-03-26 19:09:48.260][biodb::testThat]
biodb.INFO [2024-03-26 19:09:48.262][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-26 19:09:48.263][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:48.265][biodb::testThat]
biodb.INFO [2024-03-26 19:09:48.277][biodb::testThat]
biodb.INFO [2024-03-26 19:09:48.278][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-26 19:09:48.280][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:48.281][biodb::testThat]
biodb.DEBUG[2024-03-26 19:09:48.288][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-03-26 19:09:49.006][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-03-26 19:09:50.228][biodb::testThat]
biodb.INFO [2024-03-26 19:09:50.230][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-26 19:09:50.231][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:50.233][biodb::testThat]
biodb.DEBUG[2024-03-26 19:09:50.672][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[2024-03-26 19:09:51.106][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:51.108][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:51.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.111][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.112][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:51.114][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:51.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.117][ef$get] fields variable is a list.
biodb.INFO [2024-03-26 19:09:51.120][biodb::testThat]
biodb.INFO [2024-03-26 19:09:51.121][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2024-03-26 19:09:51.122][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:09:51.124][biodb::testThat]
biodb.TRACE[2024-03-26 19:09:51.142][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:51.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:51.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:51.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:51.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.155][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:51.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:51.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:51.296][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[2024-03-26 19:09:51.301][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:51.303][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:09:51.305][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:51.307][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-26 19:09:51.412][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[2024-03-26 19:09:51.416][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:51.418][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:09:51.420][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:51.422][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-03-26 19:09:51.448][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-26 19:09:51.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-26 19:09:51.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:51.483][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:51.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:51.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:51.499][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[2024-03-26 19:09:51.505][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:51.507][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-26 19:09:51.509][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:51.512][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-26 19:09:51.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:51.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:51.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:51.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:51.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:51.530][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:51.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:51.534][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-03-26 19:09:51.615][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:51.617][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-03-26 19:09:51.619][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:09:51.620][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:09:51.621][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:51.623][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:51.624][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:09:51.625][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:09:51.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:51.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:51.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:51.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:51.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:51.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:51.645][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.DEBUG[2024-03-26 19:09:51.647][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-03-26 19:09:51.651][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:09:51.653][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:09:51.655][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-03-26 19:09:52.364][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-03-26 19:09:52.770][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:09:52.773][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-03-26 19:09:52.795][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-03-26 19:09:52.799][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-03-26 19:09:52.802][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:09:52.804][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:52.806][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:52.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:52.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:52.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:52.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:52.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:52.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:52.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:52.827][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:52.828][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:52.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.831][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:52.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:52.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.838][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:52.839][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:52.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.842][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.843][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:52.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:52.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.849][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:52.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:52.852][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.853][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:52.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:52.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.861][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:52.862][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:52.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.865][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:52.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:52.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.873][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:52.874][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:52.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.877][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:52.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:52.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.884][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:52.886][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:52.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.889][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.891][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:52.892][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:52.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.895][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.897][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:52.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:52.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.916][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:52.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:52.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.922][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:52.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:52.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.929][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:52.931][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:52.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.933][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:52.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:52.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.941][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:52.943][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:52.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.946][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.948][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:52.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:52.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.954][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:52.956][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:52.957][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.958][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.960][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:52.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:52.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:52.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:52.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:52.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:52.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:52.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:52.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:52.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:52.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:52.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:52.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:52.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:52.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:52.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:52.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:53.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:53.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:53.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:53.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:53.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:53.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:53.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:53.023][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-03-26 19:09:53.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:53.058][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[2024-03-26 19:09:53.068][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:53.070][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-26 19:09:53.072][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:53.074][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-26 19:09:53.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:53.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:53.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:53.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:53.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:53.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:53.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:53.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:53.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:53.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:53.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:53.143][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:53.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:53.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:53.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:53.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:53.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:53.174][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-03-26 19:09:53.176][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:53.178][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-03-26 19:09:53.180][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:09:53.182][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:09:53.184][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:53.185][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:53.187][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:09:53.188][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:09:53.210][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:53.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:53.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:53.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:53.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:53.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:53.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:53.229][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-03-26 19:09:53.255][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:09:53.257][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:09:53.283][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-03-26 19:09:53.687][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-03-26 19:09:54.086][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:09:54.089][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-03-26 19:09:54.094][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-03-26 19:09:54.098][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-03-26 19:09:54.101][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:09:54.103][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:54.105][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:54.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:54.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:54.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:54.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:54.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:54.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:54.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:54.135][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.136][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.139][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.147][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:54.148][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:54.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.150][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.152][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:54.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:54.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.159][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:54.160][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:54.161][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.163][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.165][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:54.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:54.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.171][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:54.173][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:54.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.175][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:54.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:54.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.182][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:54.183][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:54.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.186][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.187][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:54.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:54.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.193][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:54.195][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:54.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.198][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.200][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:54.201][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.204][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.206][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:54.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.211][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:54.213][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:54.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.216][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:54.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:54.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.223][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:54.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:54.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.228][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:54.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:54.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.237][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:54.238][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:54.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.241][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.243][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:54.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:54.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.250][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:54.251][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:54.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.253][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.255][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:54.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:54.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:54.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:54.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:54.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:54.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:54.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:54.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:54.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:54.328][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-03-26 19:09:54.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:54.383][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[2024-03-26 19:09:54.388][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:09:54.390][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:09:54.407][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:09:54.409][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-26 19:09:54.413][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:54.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:54.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:54.435][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:54.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:54.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:54.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:54.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:54.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:54.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:54.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:54.459][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:54.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:54.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:54.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:54.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:54.472][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:54.473][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.DEBUG[2024-03-26 19:09:54.475][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-03-26 19:09:54.476][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:54.479][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-03-26 19:09:54.481][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:09:54.482][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:09:54.484][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:54.485][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:54.487][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:09:54.488][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:09:54.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:54.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:54.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:54.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:54.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:54.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:54.509][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[2024-03-26 19:09:54.511][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-03-26 19:09:54.516][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:09:54.518][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:09:54.519][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-03-26 19:09:54.921][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-03-26 19:09:55.321][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:09:55.324][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-03-26 19:09:55.329][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-03-26 19:09:55.334][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-03-26 19:09:55.336][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:09:55.338][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:55.340][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:55.354][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:55.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:55.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:55.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:55.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:55.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:55.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:55.374][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.376][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.377][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.378][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.386][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:55.387][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:55.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.390][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.392][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:55.393][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:55.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.396][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.398][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:55.399][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:55.400][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.402][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.404][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:55.405][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:55.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.408][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.410][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:55.411][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:55.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.414][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.416][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:55.417][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.420][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.422][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:55.423][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:55.424][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.426][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.427][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:55.429][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:55.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.432][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.434][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:55.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:55.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.439][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:55.441][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:55.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.444][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.446][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:55.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:55.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.451][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:55.453][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:55.454][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.456][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:55.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:55.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:55.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:55.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:55.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:55.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:55.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:55.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:55.514][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-03-26 19:09:55.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:55.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:55.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:55.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:55.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:55.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:55.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:55.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:55.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:55.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:55.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:55.577][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-03-26 19:09:55.579][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:55.581][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-03-26 19:09:55.583][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:09:55.584][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:09:55.586][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:55.588][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:55.589][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:09:55.591][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:09:55.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:55.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:55.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:55.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:55.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:55.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:55.610][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[2024-03-26 19:09:55.612][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-03-26 19:09:55.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:09:55.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:09:55.621][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-03-26 19:09:56.040][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-03-26 19:09:56.446][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:09:56.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-03-26 19:09:56.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-03-26 19:09:56.459][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-03-26 19:09:56.461][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:09:56.463][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:56.465][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:56.467][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:56.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:56.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:56.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:56.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:56.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:56.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:56.486][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.487][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.489][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.497][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:56.498][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:56.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.501][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.503][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:56.504][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:56.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.507][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.509][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:56.510][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:56.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.513][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.515][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:56.516][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:56.518][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.519][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.521][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:56.522][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:56.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.525][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.526][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:56.528][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.529][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.531][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.533][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:56.535][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:56.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.538][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.540][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:56.542][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:56.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.544][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.547][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:56.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.553][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:56.555][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:56.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.557][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:56.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.565][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:56.574][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:56.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.581][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:56.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:56.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:56.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:56.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:56.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:56.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.613][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:56.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:56.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:56.642][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-03-26 19:09:56.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:56.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:56.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:56.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:56.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:56.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:56.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:56.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:56.687][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:56.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:56.690][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-03-26 19:09:56.692][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:56.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-03-26 19:09:56.696][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:09:56.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:09:56.699][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:56.701][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:56.702][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:09:56.704][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:09:56.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:56.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:56.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:56.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:56.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:56.723][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:56.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:56.727][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-03-26 19:09:56.731][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:09:56.733][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:09:56.735][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-03-26 19:09:57.142][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-03-26 19:09:57.572][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:09:57.575][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-03-26 19:09:57.580][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-03-26 19:09:57.584][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-03-26 19:09:57.587][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:09:57.588][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:57.590][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:57.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:57.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:57.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:57.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:57.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:57.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:57.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:57.621][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.623][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.626][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.634][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:57.635][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:57.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.638][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.639][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:57.641][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:57.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.644][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.646][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:57.647][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:57.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.649][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.651][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:57.653][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:57.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.655][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.657][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:57.658][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:57.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.660][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.662][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:57.663][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.664][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.665][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:57.668][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:57.670][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.671][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.673][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:57.674][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:57.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.677][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.679][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:57.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:57.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.684][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:57.685][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:57.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.687][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.689][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:57.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:57.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.693][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:57.694][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:57.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.696][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:57.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:57.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:57.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:57.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:57.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:57.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:57.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:57.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:57.745][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-03-26 19:09:57.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:57.769][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:57.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:57.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:57.781][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:57.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:57.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:57.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:57.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:57.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:57.796][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:57.797][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-03-26 19:09:57.799][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:57.803][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-03-26 19:09:57.804][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:09:57.806][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:09:57.807][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:57.809][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:57.810][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:09:57.812][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:09:57.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:57.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:57.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:57.826][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:57.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:57.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:57.830][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[2024-03-26 19:09:57.832][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-03-26 19:09:57.835][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:09:57.836][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:09:57.838][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-03-26 19:09:58.242][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-03-26 19:09:58.639][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:09:58.642][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-03-26 19:09:58.647][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-03-26 19:09:58.651][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-03-26 19:09:58.654][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:09:58.656][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:58.658][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:58.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:58.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:58.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:58.673][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:58.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:58.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:58.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:58.681][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.682][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.684][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.685][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.693][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:58.694][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:58.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.697][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.698][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:58.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:58.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.704][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:58.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:58.707][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.708][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:58.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:58.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.717][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:58.718][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:58.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.719][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:58.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:58.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.726][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:58.727][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:58.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.729][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.731][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:58.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:58.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.737][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:58.739][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:58.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.741][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.743][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:58.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:58.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.749][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:58.750][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.753][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.755][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:58.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:58.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:58.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.773][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:58.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:58.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.781][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:58.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:58.784][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.785][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.787][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:58.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:58.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.793][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:58.794][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:58.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.797][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.799][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:58.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:58.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.805][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:58.806][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:58.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.810][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.812][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:58.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:58.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:58.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:58.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:58.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:58.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:58.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:58.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:58.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:58.890][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-03-26 19:09:58.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:58.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:58.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:09:58.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:58.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:58.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:58.916][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:58.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:58.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:58.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:58.921][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-03-26 19:09:58.922][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:09:58.923][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-03-26 19:09:58.925][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:09:58.927][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:09:58.928][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:09:58.929][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:09:58.931][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:09:58.933][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:09:58.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:58.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:58.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:58.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:58.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:58.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:58.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:09:58.952][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-03-26 19:09:58.956][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:09:58.957][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:09:58.959][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-03-26 19:09:59.354][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-03-26 19:09:59.788][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:09:59.792][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-03-26 19:09:59.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-03-26 19:09:59.801][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-03-26 19:09:59.804][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:09:59.805][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:09:59.807][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:09:59.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:09:59.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:09:59.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:09:59.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:09:59.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:09:59.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:09:59.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:09:59.828][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:59.842][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:59.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.845][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:59.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:59.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.851][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:59.852][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:59.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.855][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.857][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:09:59.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:09:59.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.866][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:59.867][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:59.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.869][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.871][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:09:59.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:09:59.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.877][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:59.879][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:59.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.881][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:09:59.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:09:59.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.889][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:59.891][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:59.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.893][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:09:59.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:09:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.901][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:59.903][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:59.904][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.906][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.907][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:59.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:09:59.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.912][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:59.914][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:59.915][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.916][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.918][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:09:59.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:09:59.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.924][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:59.926][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:59.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.928][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:59.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:09:59.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.936][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:59.937][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:59.939][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.940][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:09:59.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:09:59.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.948][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:59.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:59.951][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.952][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.953][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:09:59.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:09:59.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.959][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:59.960][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:59.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.963][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.965][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:09:59.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:09:59.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:59.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:59.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:59.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:59.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:09:59.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:09:59.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:09:59.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:09:59.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:09:59.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:09:59.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:00.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:00.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:00.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:00.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:00.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:00.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:00.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:00.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:00.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:00.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:00.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:00.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:00.037][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-03-26 19:10:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:00.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:00.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.044][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:00.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:00.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:00.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:00.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:00.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:00.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:00.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:00.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:00.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:00.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:00.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:00.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:00.073][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-03-26 19:10:00.074][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:00.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-03-26 19:10:00.078][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:00.080][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:00.081][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:00.083][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:00.084][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:00.086][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:00.089][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:00.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:00.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:00.100][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:00.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:00.103][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:00.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:00.106][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-03-26 19:10:00.110][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:00.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:00.113][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-03-26 19:10:00.507][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-03-26 19:10:00.952][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:00.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-03-26 19:10:00.962][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-03-26 19:10:00.966][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-03-26 19:10:00.969][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:00.971][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:00.972][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:00.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:00.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:00.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:00.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:00.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:00.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:00.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:00.994][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:00.995][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:00.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:00.998][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.006][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:01.007][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:01.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.010][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.012][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:01.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:01.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.018][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:01.019][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:01.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.022][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:01.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:01.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.042][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:01.043][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:01.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.046][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:01.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:01.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.053][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:01.054][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:01.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.057][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:01.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:01.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.065][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:01.066][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:01.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.069][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.071][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:01.073][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.075][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:01.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.081][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:01.083][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:01.084][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.085][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:01.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:01.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.094][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:01.096][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:01.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.099][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.101][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:01.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:01.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.108][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:01.109][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:01.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.112][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.113][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:01.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:01.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.119][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:01.120][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:01.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.123][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:01.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:01.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:01.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:01.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:01.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:01.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:01.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:01.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:01.187][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-03-26 19:10:01.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:01.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:01.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:01.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:01.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:01.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:01.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:01.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:01.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:01.227][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:01.228][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[2024-03-26 19:10:01.230][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-03-26 19:10:01.231][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:01.233][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-03-26 19:10:01.235][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:01.236][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:01.238][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:01.239][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:01.240][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:01.242][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:01.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:01.247][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:01.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:01.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:01.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:01.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:01.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:01.263][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-03-26 19:10:01.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:01.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:01.270][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-03-26 19:10:01.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-03-26 19:10:02.083][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:02.086][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-03-26 19:10:02.091][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-03-26 19:10:02.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-03-26 19:10:02.098][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:02.100][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:02.102][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:02.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:02.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:02.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:02.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:02.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:02.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:02.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:02.123][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.124][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.128][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.136][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:02.138][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:02.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.141][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.142][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:02.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:02.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.148][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:02.149][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:02.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.152][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.154][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:02.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:02.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.160][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:02.162][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:02.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.164][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:02.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:02.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.173][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:02.174][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:02.175][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.177][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.179][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:02.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:02.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.185][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:02.187][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:02.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.189][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.191][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:02.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.195][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.197][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:02.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.204][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:02.206][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:02.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.208][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:02.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:02.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.217][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:02.218][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:02.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.221][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:02.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:02.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.236][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:02.243][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:02.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.247][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.249][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:02.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:02.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.255][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:02.256][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:02.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.259][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.261][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:02.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:02.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:02.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:02.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:02.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:02.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:02.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:02.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:02.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:02.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:02.330][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-03-26 19:10:02.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:02.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:02.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:02.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:02.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:02.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:02.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:02.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:02.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:02.383][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:02.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:02.386][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-03-26 19:10:02.387][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:02.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-03-26 19:10:02.390][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:02.392][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:02.393][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:02.395][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:02.396][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:02.398][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:02.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:02.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:02.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:02.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:02.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:02.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:02.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:02.418][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-03-26 19:10:02.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:02.424][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:02.426][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-03-26 19:10:02.839][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-03-26 19:10:03.235][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:03.238][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-03-26 19:10:03.244][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-03-26 19:10:03.248][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-03-26 19:10:03.271][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:03.273][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:03.275][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:03.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:03.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:03.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:03.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:03.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:03.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:03.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:03.307][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.312][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.318][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:03.320][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:03.321][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.322][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.324][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:03.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:03.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.330][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:03.332][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:03.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.334][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:03.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:03.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.342][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:03.344][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:03.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.346][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:03.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:03.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.353][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:03.354][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:03.355][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.357][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.358][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:03.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:03.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.384][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:03.386][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:03.387][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.389][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.391][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:03.392][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.393][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.395][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.396][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:03.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.406][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:03.407][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:03.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.410][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:03.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:03.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.417][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:03.418][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:03.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.420][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.422][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:03.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:03.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.428][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:03.429][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:03.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.431][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.433][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:03.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:03.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.439][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:03.440][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:03.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.443][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.444][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:03.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:03.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:03.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:03.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:03.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:03.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:03.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:03.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:03.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:03.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:03.532][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-03-26 19:10:03.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:03.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:03.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:03.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:03.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:03.553][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:03.554][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:03.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:03.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:03.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:03.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:03.569][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-03-26 19:10:03.571][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:03.573][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-03-26 19:10:03.575][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:03.576][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:03.578][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:03.579][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:03.581][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:03.582][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:03.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:03.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:03.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:03.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:03.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:03.621][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:03.622][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[2024-03-26 19:10:03.625][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-03-26 19:10:03.628][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:03.630][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:03.633][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-03-26 19:10:04.031][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-03-26 19:10:04.429][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:04.432][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-03-26 19:10:04.438][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-03-26 19:10:04.442][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-03-26 19:10:04.445][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:04.447][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:04.449][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:04.452][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:04.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:04.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:04.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:04.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:04.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:04.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:04.472][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.474][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.477][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.484][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:04.486][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:04.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.488][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.490][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:04.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:04.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.495][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:04.497][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:04.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.500][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.501][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:04.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:04.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.507][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:04.509][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:04.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.512][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:04.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:04.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.519][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:04.521][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:04.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.523][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:04.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:04.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.543][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:04.545][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:04.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.548][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.550][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:04.551][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.554][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:04.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.563][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:04.565][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:04.566][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.567][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:04.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:04.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.574][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:04.576][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:04.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.578][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:04.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:04.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.586][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:04.588][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:04.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.591][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.592][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:04.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:04.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.598][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:04.599][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:04.600][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.601][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:04.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:04.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:04.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:04.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.625][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:04.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:04.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:04.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:04.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:04.659][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-03-26 19:10:04.660][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:04.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:04.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:04.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:04.675][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:04.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:04.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:04.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:04.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:04.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:04.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:04.691][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-03-26 19:10:04.692][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:04.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-03-26 19:10:04.696][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:04.698][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:04.699][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:04.701][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:04.702][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:04.703][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:04.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:04.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:04.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:04.725][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:04.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:04.727][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:04.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:04.730][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-03-26 19:10:04.733][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:04.735][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:04.737][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-03-26 19:10:05.135][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-03-26 19:10:05.530][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:05.533][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-03-26 19:10:05.537][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-03-26 19:10:05.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-03-26 19:10:05.543][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:05.546][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:05.547][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:05.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:05.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:05.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:05.559][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:05.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:05.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:05.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:05.565][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.568][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.570][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.575][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:05.576][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:05.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.578][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.579][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:05.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:05.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.585][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:05.586][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:05.587][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.589][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.591][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:05.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:05.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.596][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:05.598][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:05.598][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.600][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.601][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:05.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:05.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.606][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:05.606][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:05.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.609][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:05.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:05.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.616][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:05.618][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:05.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.620][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.621][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:05.623][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.624][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.625][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.626][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:05.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.631][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:05.633][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:05.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.635][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:05.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:05.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.641][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:05.643][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:05.644][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.645][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.647][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:05.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:05.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.652][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:05.654][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:05.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.657][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.658][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:05.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:05.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.663][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:05.665][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:05.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.667][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.668][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:05.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:05.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:05.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:05.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:05.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:05.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:05.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:05.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.708][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.725][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:05.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:05.732][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-03-26 19:10:05.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:05.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:05.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:05.750][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:05.751][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:05.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:05.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:05.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:05.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:05.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:05.763][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-03-26 19:10:05.765][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:05.767][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-03-26 19:10:05.768][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:05.770][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:05.771][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:05.772][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:05.773][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:05.774][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:05.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:05.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:05.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:05.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:05.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:05.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:05.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:05.791][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-03-26 19:10:05.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:05.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:05.797][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-03-26 19:10:06.193][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-03-26 19:10:06.591][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:06.594][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-03-26 19:10:06.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-03-26 19:10:06.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-03-26 19:10:06.604][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:06.606][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:06.607][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:06.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:06.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:06.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:06.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:06.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:06.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:06.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:06.622][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.624][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.625][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.626][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.633][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:06.646][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:06.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.649][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.651][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:06.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:06.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.655][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:06.656][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:06.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.659][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.660][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:06.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:06.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.664][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:06.665][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:06.666][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.668][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.670][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:06.671][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:06.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.673][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.675][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:06.676][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:06.677][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.678][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.679][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:06.680][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.682][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.683][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:06.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:06.689][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:06.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.692][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:06.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:06.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.698][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:06.699][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:06.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.701][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.703][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:06.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:06.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.707][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:06.708][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:06.709][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.710][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.712][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:06.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:06.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.717][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:06.718][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:06.719][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.720][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:06.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:06.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:06.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:06.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:06.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:06.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:06.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:06.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:06.770][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-03-26 19:10:06.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:06.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:06.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:06.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:06.786][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:06.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:06.789][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:06.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:06.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:06.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:06.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:06.806][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-03-26 19:10:06.807][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:06.809][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-03-26 19:10:06.810][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:06.811][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:06.813][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:06.814][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:06.815][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:06.817][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:06.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:06.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:06.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:06.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:06.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:06.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:06.834][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.DEBUG[2024-03-26 19:10:06.836][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-03-26 19:10:06.840][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:06.841][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:06.842][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-03-26 19:10:07.249][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-03-26 19:10:07.644][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:07.647][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-03-26 19:10:07.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-03-26 19:10:07.657][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-03-26 19:10:07.660][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:07.661][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:07.663][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:07.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:07.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:07.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:07.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:07.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:07.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:07.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:07.683][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.685][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.688][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.695][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:07.696][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:07.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.698][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.700][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:07.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:07.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.705][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:07.707][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:07.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.709][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.711][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:07.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:07.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.716][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:07.717][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:07.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.719][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.720][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:07.722][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:07.722][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.724][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.725][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:07.726][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:07.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.729][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.731][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:07.732][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.734][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.735][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.737][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:07.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.742][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:07.743][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:07.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.745][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:07.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:07.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.751][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:07.752][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:07.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.755][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.756][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:07.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:07.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.762][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:07.763][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:07.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.765][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.767][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:07.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:07.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.783][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:07.785][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:07.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.787][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:07.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:07.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:07.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:07.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:07.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:07.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:07.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:07.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:07.844][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-03-26 19:10:07.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:07.855][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:07.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:07.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:07.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:07.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:07.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:07.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:07.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:07.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:07.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:07.876][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-03-26 19:10:07.878][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:07.880][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-03-26 19:10:07.883][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:07.884][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:07.886][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:07.887][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:07.888][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:07.889][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:07.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:07.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:07.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:07.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:07.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:07.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:07.907][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[2024-03-26 19:10:07.908][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-03-26 19:10:07.912][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:07.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:07.915][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-03-26 19:10:08.310][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-03-26 19:10:08.723][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:08.727][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-03-26 19:10:08.732][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-03-26 19:10:08.736][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-03-26 19:10:08.738][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:08.740][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:08.742][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:08.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:08.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:08.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:08.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:08.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:08.758][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:08.759][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:08.772][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:08.788][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:08.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:08.791][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:08.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:08.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:08.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:08.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:08.822][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:08.832][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:08.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:08.889][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:08.910][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:08.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:08.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:08.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:08.960][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:08.962][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:08.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:08.984][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:08.986][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:08.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.011][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:09.013][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:09.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.016][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:09.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:09.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.024][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:09.026][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:09.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.028][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.030][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:09.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:09.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.036][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:09.037][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:09.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.040][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.041][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:09.043][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.046][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.048][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:09.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.053][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:09.055][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:09.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.057][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:09.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:09.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.064][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:09.066][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:09.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.068][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.070][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:09.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:09.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.076][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:09.078][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:09.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.080][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.082][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:09.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:09.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.088][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:09.090][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:09.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.093][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.095][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:09.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:09.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:09.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:09.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:09.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:09.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:09.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:09.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:09.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:09.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:09.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:09.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:09.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:09.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:09.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:09.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:09.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:09.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:09.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.155][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:09.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:09.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:09.167][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-03-26 19:10:09.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:09.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:09.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:09.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:09.186][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:09.188][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:09.189][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:09.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:09.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:09.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:09.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:09.203][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-03-26 19:10:09.205][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:09.207][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-03-26 19:10:09.208][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:09.210][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:09.211][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:09.213][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:09.214][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:09.215][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:09.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:09.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:09.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:09.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:09.231][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:09.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:09.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:09.235][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-03-26 19:10:09.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:09.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:09.243][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-03-26 19:10:09.665][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-03-26 19:10:10.061][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:10.063][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-03-26 19:10:10.067][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-03-26 19:10:10.071][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-03-26 19:10:10.073][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:10.075][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:10.077][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:10.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:10.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:10.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:10.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:10.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:10.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:10.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:10.096][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.098][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.100][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.106][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:10.108][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:10.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.110][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.112][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:10.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:10.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.117][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:10.118][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:10.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.121][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.122][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:10.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:10.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.127][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:10.128][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:10.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.131][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:10.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:10.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.138][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:10.139][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:10.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.142][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:10.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:10.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.149][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:10.150][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:10.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.166][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.168][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:10.171][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.174][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.176][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:10.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.182][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:10.183][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:10.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.186][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:10.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:10.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.193][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:10.194][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:10.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.197][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:10.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:10.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.205][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:10.207][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:10.208][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.210][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.212][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:10.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:10.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.219][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:10.221][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:10.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.223][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.226][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:10.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:10.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:10.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:10.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:10.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:10.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:10.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:10.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:10.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:10.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:10.285][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-03-26 19:10:10.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:10.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:10.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:10.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:10.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:10.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:10.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:10.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:10.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:10.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:10.316][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[2024-03-26 19:10:10.317][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-03-26 19:10:10.319][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:10.322][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-03-26 19:10:10.323][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:10.325][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:10.326][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:10.327][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:10.329][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:10.330][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:10.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:10.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:10.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:10.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:10.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:10.355][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:10.357][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[2024-03-26 19:10:10.358][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-03-26 19:10:10.362][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:10.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:10.365][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-03-26 19:10:10.758][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-03-26 19:10:11.164][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:11.167][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-03-26 19:10:11.171][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-03-26 19:10:11.175][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-03-26 19:10:11.178][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:11.179][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:11.181][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:11.184][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:11.185][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:11.187][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:11.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:11.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:11.197][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:11.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:11.202][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.203][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.206][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.214][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:11.215][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:11.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.217][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.219][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:11.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:11.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.225][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:11.227][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:11.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.229][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:11.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:11.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.236][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:11.237][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:11.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.239][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.241][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:11.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:11.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.246][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:11.248][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:11.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.250][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:11.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:11.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.256][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:11.257][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:11.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.259][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.260][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:11.262][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.264][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.266][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:11.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.270][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:11.272][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:11.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.274][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:11.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:11.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.281][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:11.282][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:11.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.284][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.286][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:11.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:11.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.291][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:11.293][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:11.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.295][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.297][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:11.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:11.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.303][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:11.305][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:11.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.308][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.310][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:11.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:11.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:11.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:11.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.335][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:11.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:11.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:11.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:11.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.368][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:11.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:11.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:11.389][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-03-26 19:10:11.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:11.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:11.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:11.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:11.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:11.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:11.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:11.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:11.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:11.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:11.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:11.425][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-03-26 19:10:11.426][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:11.429][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-03-26 19:10:11.431][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:11.432][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:11.434][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:11.435][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:11.437][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:11.438][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:11.442][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:11.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:11.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:11.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:11.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:11.455][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:11.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:11.457][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-03-26 19:10:11.461][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:11.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:11.465][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-03-26 19:10:11.890][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-03-26 19:10:12.306][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:12.309][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-03-26 19:10:12.313][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-03-26 19:10:12.317][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-03-26 19:10:12.320][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:12.322][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:12.323][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:12.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:12.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:12.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:12.336][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:12.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:12.339][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:12.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:12.342][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.344][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.347][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.364][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:12.365][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:12.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.368][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.370][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:12.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:12.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.375][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:12.377][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:12.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.380][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:12.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:12.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.387][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:12.388][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:12.390][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.391][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:12.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:12.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.397][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:12.398][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:12.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.400][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:12.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:12.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.406][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:12.407][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:12.408][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.409][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.411][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:12.412][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.415][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.416][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:12.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.422][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:12.424][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:12.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.426][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:12.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:12.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.433][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:12.434][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:12.435][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.436][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:12.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:12.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.442][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:12.443][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:12.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.444][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.445][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:12.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:12.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.449][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:12.450][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:12.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.452][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.453][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:12.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:12.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:12.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:12.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:12.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:12.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:12.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:12.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:12.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:12.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:12.505][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-03-26 19:10:12.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:12.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:12.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:12.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:12.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:12.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:12.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:12.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:12.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:12.543][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:12.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:12.545][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-03-26 19:10:12.546][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:12.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-03-26 19:10:12.549][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:12.550][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:12.551][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:12.552][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:12.553][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:12.554][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:12.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:12.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:12.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:12.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:12.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:12.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:12.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:12.572][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-03-26 19:10:12.575][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:12.576][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:12.578][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-03-26 19:10:12.984][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-03-26 19:10:13.396][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:13.399][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-03-26 19:10:13.404][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-03-26 19:10:13.409][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-03-26 19:10:13.411][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:13.412][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:13.414][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:13.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:13.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:13.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:13.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:13.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:13.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:13.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:13.434][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.436][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.439][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.445][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:13.446][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:13.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.449][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.450][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:13.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:13.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.456][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:13.457][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:13.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.459][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.461][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:13.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:13.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.467][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:13.468][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:13.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.471][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:13.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:13.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.478][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:13.479][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:13.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.482][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:13.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:13.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.490][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:13.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:13.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.494][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.496][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:13.497][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.499][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.501][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:13.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.519][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:13.521][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:13.522][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.523][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.525][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:13.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:13.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.529][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:13.531][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:13.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.533][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:13.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:13.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.540][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:13.541][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:13.542][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.543][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.545][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:13.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.549][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:13.551][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:13.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.553][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.554][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:13.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:13.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:13.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:13.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:13.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:13.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:13.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:13.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:13.611][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-03-26 19:10:13.613][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:13.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:13.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:13.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:13.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:13.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:13.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:13.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:13.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:13.641][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:13.642][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[2024-03-26 19:10:13.645][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-03-26 19:10:13.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:13.651][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-03-26 19:10:13.655][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:13.657][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:13.659][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:13.661][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:13.662][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:13.663][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:13.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:13.669][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:13.669][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:13.676][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:13.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:13.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:13.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:13.681][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-03-26 19:10:13.692][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:13.693][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:13.695][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-03-26 19:10:14.176][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-03-26 19:10:14.574][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:14.577][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-03-26 19:10:14.582][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-03-26 19:10:14.585][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-03-26 19:10:14.587][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:14.588][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:14.589][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:14.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:14.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:14.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:14.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:14.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:14.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:14.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:14.609][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.611][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.614][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.621][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:14.622][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:14.623][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.624][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.629][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:14.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:14.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.632][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.633][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:14.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:14.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.637][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:14.638][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:14.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.640][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:14.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:14.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.645][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:14.646][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:14.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.648][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:14.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:14.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.653][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:14.655][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:14.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.657][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.658][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:14.659][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.661][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.662][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:14.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.666][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:14.667][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:14.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.668][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:14.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:14.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.675][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:14.676][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:14.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.679][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:14.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:14.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.687][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:14.689][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:14.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.691][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.692][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:14.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:14.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.696][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:14.697][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:14.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.699][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.701][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:14.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:14.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:14.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:14.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:14.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:14.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:14.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:14.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:14.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:14.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:14.761][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-03-26 19:10:14.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.768][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:14.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:14.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:14.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:14.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:14.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:14.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:14.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:14.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:14.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:14.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:14.796][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-03-26 19:10:14.797][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:14.798][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-03-26 19:10:14.800][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:14.802][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:14.804][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:14.805][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:14.807][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:14.808][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:14.812][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:14.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:14.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:14.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:14.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:14.825][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:14.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:14.829][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-03-26 19:10:14.833][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:14.834][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:14.837][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-03-26 19:10:15.277][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-03-26 19:10:15.681][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:15.684][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-03-26 19:10:15.688][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-03-26 19:10:15.692][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-03-26 19:10:15.694][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:15.696][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:15.698][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:15.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:15.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:15.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:15.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:15.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:15.712][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:15.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:15.715][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.717][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.719][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.726][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:15.727][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:15.728][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.730][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.732][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:15.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:15.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.749][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:15.751][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:15.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.754][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:15.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:15.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.761][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:15.762][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:15.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.764][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:15.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.771][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:15.772][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:15.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.773][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:15.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:15.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.780][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:15.782][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:15.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.784][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.786][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:15.787][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.789][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.790][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:15.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.795][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:15.796][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:15.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.799][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:15.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:15.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.806][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:15.807][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:15.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.809][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:15.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:15.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.814][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:15.815][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:15.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.816][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.817][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:15.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:15.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.821][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:15.822][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:15.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.824][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:15.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:15.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:15.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:15.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:15.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:15.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:15.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:15.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:15.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:15.872][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-03-26 19:10:15.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:15.923][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[2024-03-26 19:10:15.929][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:15.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:10:15.934][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:15.936][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-26 19:10:15.939][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:15.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:15.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:15.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:15.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:15.950][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:15.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:15.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:15.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:15.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:15.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:15.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:15.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:15.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:15.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:15.982][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:15.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:15.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:15.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.001][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.016][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.018][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.020][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.TRACE[2024-03-26 19:10:16.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.027][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.031][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.044][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.058][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.094][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.099][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.129][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.161][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.177][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[2024-03-26 19:10:16.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.196][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.239][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.279][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.280][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.TRACE[2024-03-26 19:10:16.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.301][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.381][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[2024-03-26 19:10:16.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.399][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.446][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[2024-03-26 19:10:16.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.475][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.485][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.487][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.TRACE[2024-03-26 19:10:16.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.540][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.541][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.550][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.553][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.574][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.587][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.591][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.605][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.617][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.738][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[2024-03-26 19:10:16.743][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:16.745][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2024-03-26 19:10:16.747][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:16.749][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2024-03-26 19:10:16.753][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[2024-03-26 19:10:16.757][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:16.759][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2024-03-26 19:10:16.761][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:16.764][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2024-03-26 19:10:16.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.770][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:16.785][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-03-26 19:10:16.787][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:16.790][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-03-26 19:10:16.792][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:16.794][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2024-03-26 19:10:16.796][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:16.798][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:16.799][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:16.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:16.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:16.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:16.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:16.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:16.816][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:16.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:16.821][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.822][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.825][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.831][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:16.832][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:16.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.834][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.835][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:16.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:16.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.848][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:16.850][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:16.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.852][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.854][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:16.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:16.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.859][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:16.860][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:16.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.863][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.865][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:16.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:16.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.870][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:16.871][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:16.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.873][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.875][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:16.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:16.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.879][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:16.880][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:16.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.883][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:16.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.890][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:16.891][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.894][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.896][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:16.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:16.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.899][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.900][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.903][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:16.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.910][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:16.911][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:16.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.914][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.915][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:16.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:16.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.920][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:16.921][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:16.922][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.923][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.925][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:16.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:16.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.930][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:16.931][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:16.932][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.933][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.935][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:16.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:16.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:16.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:16.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:16.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:16.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:16.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:16.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:16.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:16.997][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-03-26 19:10:16.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.025][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.037][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[2024-03-26 19:10:17.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.063][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:17.065][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-03-26 19:10:17.066][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:17.068][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-03-26 19:10:17.069][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:17.071][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2024-03-26 19:10:17.073][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:17.074][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:17.075][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:17.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.090][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.095][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.097][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.099][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.104][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:17.105][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:17.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.107][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.109][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:17.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:17.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.113][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:17.115][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:17.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.117][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.118][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:17.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:17.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.121][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:17.123][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:17.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.125][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:17.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:17.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.130][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:17.131][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:17.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.133][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:17.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:17.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.138][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:17.139][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:17.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.141][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.142][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:17.144][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:17.145][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.146][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.148][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:17.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:17.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.152][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.153][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.156][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.162][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:17.163][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:17.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.173][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:17.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:17.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.181][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:17.183][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:17.184][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.185][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:17.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:17.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.190][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:17.191][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:17.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.193][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.195][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:17.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:17.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:17.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:17.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:17.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:17.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:17.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:17.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:17.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:17.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.248][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-03-26 19:10:17.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.291][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[2024-03-26 19:10:17.295][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:17.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:10:17.298][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:17.299][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-26 19:10:17.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.316][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.TRACE[2024-03-26 19:10:17.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.327][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.353][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[2024-03-26 19:10:17.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.416][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.430][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[2024-03-26 19:10:17.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.461][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.475][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.TRACE[2024-03-26 19:10:17.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.528][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.539][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.541][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[2024-03-26 19:10:17.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.611][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.617][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.625][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.646][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.658][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.707][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.749][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[2024-03-26 19:10:17.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.791][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.804][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.833][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.834][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.TRACE[2024-03-26 19:10:17.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.871][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.872][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.TRACE[2024-03-26 19:10:17.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.898][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.899][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.TRACE[2024-03-26 19:10:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.928][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:17.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:17.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:17.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:17.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:17.971][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[2024-03-26 19:10:17.974][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:17.976][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-03-26 19:10:17.978][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:17.980][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-03-26 19:10:17.983][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:17.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:17.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:17.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:17.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:17.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:17.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.077][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.TRACE[2024-03-26 19:10:18.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.111][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.128][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.156][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.173][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.195][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.229][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.254][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[2024-03-26 19:10:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.283][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.368][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.380][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.381][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.384][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.TRACE[2024-03-26 19:10:18.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.463][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.512][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.532][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.542][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.556][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.569][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.570][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[2024-03-26 19:10:18.572][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.598][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.600][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.605][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.609][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.628][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:18.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.661][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:18.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:18.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-26 19:10:18.678][biodb::testThat]
biodb.INFO [2024-03-26 19:10:18.680][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-26 19:10:18.681][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:18.683][biodb::testThat]
biodb.TRACE[2024-03-26 19:10:18.687][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-26 19:10:18.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-26 19:10:18.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:18.743][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[2024-03-26 19:10:18.746][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:18.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-26 19:10:18.749][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:18.751][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-26 19:10:18.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.774][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.781][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[2024-03-26 19:10:18.786][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:18.787][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-26 19:10:18.789][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:18.791][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-26 19:10:18.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.803][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.804][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[2024-03-26 19:10:18.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:18.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:18.848][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-26 19:10:18.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.884][private$selectFields]
biodb.TRACE[2024-03-26 19:10:18.886][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:18.887][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:18.888][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.893][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.894][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.898][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.899][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.900][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.901][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.902][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.903][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.904][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:18.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.932][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-26 19:10:18.933][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:18.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:18.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:18.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:18.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:18.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:18.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:18.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.958][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.958][private$selectFields]
biodb.TRACE[2024-03-26 19:10:18.959][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:18.961][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:18.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.963][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.964][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.967][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.968][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.970][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.972][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.974][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.975][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:18.976][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.978][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.979][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.980][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.981][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:18.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:18.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:18.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:18.998][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-26 19:10:18.999][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.013][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.014][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.TRACE[2024-03-26 19:10:19.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.027][private$selectFields]
biodb.TRACE[2024-03-26 19:10:19.028][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:19.029][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:19.030][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.031][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.211][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.213][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.216][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.219][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.220][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.221][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.222][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.223][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.225][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.226][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:19.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.242][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-26 19:10:19.243][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-26 19:10:19.244][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-26 19:10:19.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:19.347][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[2024-03-26 19:10:19.352][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:19.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-03-26 19:10:19.356][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:19.359][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-03-26 19:10:19.363][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[2024-03-26 19:10:19.368][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:19.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-03-26 19:10:19.371][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:19.374][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-03-26 19:10:19.377][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:19.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.400][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.406][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:19.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.451][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.454][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:19.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:19.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.507][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-26 19:10:19.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.552][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:19.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.572][private$selectFields]
biodb.TRACE[2024-03-26 19:10:19.573][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:19.574][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:19.575][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.577][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.578][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.581][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.583][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.584][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.586][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.587][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.588][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.590][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.591][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.593][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.595][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:19.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.609][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-26 19:10:19.610][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.612][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.613][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:19.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.689][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.690][private$selectFields]
biodb.TRACE[2024-03-26 19:10:19.691][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:19.693][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:19.694][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.696][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.697][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.699][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.700][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.701][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.703][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.705][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.713][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.715][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.717][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.718][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.720][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.721][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:19.722][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.733][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.738][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-26 19:10:19.740][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.752][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[2024-03-26 19:10:19.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.764][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.766][private$selectFields]
biodb.TRACE[2024-03-26 19:10:19.767][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:19.768][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:19.769][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.771][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.774][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.778][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.779][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.781][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:19.782][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.783][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.786][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.788][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:19.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:19.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.803][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-26 19:10:19.804][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-26 19:10:19.805][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-26 19:10:19.816][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:19.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:19.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-26 19:10:19.827][biodb::testThat]
biodb.INFO [2024-03-26 19:10:19.828][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-26 19:10:19.829][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:19.830][biodb::testThat]
biodb.TRACE[2024-03-26 19:10:19.833][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-26 19:10:19.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-26 19:10:19.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.837][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.841][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.858][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.859][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:19.876][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[2024-03-26 19:10:19.879][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:19.881][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-26 19:10:19.883][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:19.885][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-26 19:10:19.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.890][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.902][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.903][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.TRACE[2024-03-26 19:10:19.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.918][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[2024-03-26 19:10:19.921][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:19.922][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-26 19:10:19.923][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:19.924][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-26 19:10:19.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.940][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[2024-03-26 19:10:19.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:19.965][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:19.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:19.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:19.969][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[2024-03-26 19:10:19.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:19.983][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:19.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:19.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:19.989][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-26 19:10:19.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:19.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:19.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.004][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[2024-03-26 19:10:20.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.012][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.013][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.014][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.015][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.016][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.019][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.020][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.021][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.023][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.024][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.025][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.026][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.027][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.029][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.030][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.055][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-26 19:10:20.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.083][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.083][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.085][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.085][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.086][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.087][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.088][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.090][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.093][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.094][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.095][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.096][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.097][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.099][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.100][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.116][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-26 19:10:20.117][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.125][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.127][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.138][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.138][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.139][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.140][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.141][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.142][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.143][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.145][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.146][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.149][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.149][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.150][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.151][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.152][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.153][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.154][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.155][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.164][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.170][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-26 19:10:20.171][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-26 19:10:20.172][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-26 19:10:20.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.213][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.225][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:20.228][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[2024-03-26 19:10:20.231][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:20.232][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-03-26 19:10:20.234][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:20.235][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-03-26 19:10:20.238][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[2024-03-26 19:10:20.241][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:20.242][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-03-26 19:10:20.244][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:20.245][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-03-26 19:10:20.247][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.248][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.262][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.264][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.TRACE[2024-03-26 19:10:20.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.277][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.282][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.293][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.312][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.313][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.338][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-26 19:10:20.340][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.353][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[2024-03-26 19:10:20.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.366][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.368][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.369][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.370][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.372][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.373][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.375][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.378][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.379][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.381][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.384][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.387][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.388][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.390][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.392][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.393][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.408][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-26 19:10:20.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.410][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.435][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.436][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.437][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.439][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.440][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.441][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.443][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.444][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.446][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.448][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.449][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.451][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.452][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.453][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.455][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.456][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.458][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.459][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.474][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.479][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.484][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-26 19:10:20.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.511][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.512][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.514][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.515][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.516][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.518][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.519][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.522][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.523][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.524][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.526][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.527][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.528][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.530][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.531][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.533][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.534][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.548][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-26 19:10:20.550][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-26 19:10:20.551][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-26 19:10:20.563][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:20.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:20.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-26 19:10:20.573][biodb::testThat]
biodb.INFO [2024-03-26 19:10:20.574][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-26 19:10:20.575][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:20.576][biodb::testThat]
biodb.TRACE[2024-03-26 19:10:20.580][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-26 19:10:20.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-26 19:10:20.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.589][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.612][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:20.628][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[2024-03-26 19:10:20.632][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:20.634][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-03-26 19:10:20.635][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:20.637][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-03-26 19:10:20.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.669][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[2024-03-26 19:10:20.673][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:20.674][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-03-26 19:10:20.675][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:20.676][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-03-26 19:10:20.678][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.703][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:20.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.734][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-26 19:10:20.735][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.746][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.757][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.759][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.760][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.761][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.762][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.763][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.764][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.765][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.766][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.768][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.768][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.770][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.771][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.772][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.773][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.774][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.775][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.778][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.779][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.797][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-03-26 19:10:20.798][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.822][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.823][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.824][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.825][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.826][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.827][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.828][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.829][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.830][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.832][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.833][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.834][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.836][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.837][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.839][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.840][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.842][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.843][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.858][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-26 19:10:20.859][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:20.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:20.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:20.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:20.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:20.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.883][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.884][private$selectFields]
biodb.TRACE[2024-03-26 19:10:20.885][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:20.886][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:20.888][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.890][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.892][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.893][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.902][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.904][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.907][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.908][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.910][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:20.911][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.911][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.913][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.914][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.914][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:20.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.920][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:20.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.931][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-03-26 19:10:20.933][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-26 19:10:20.935][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-26 19:10:20.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:20.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:20.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:20.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:20.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:20.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:20.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:21.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:21.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:21.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:21.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:21.010][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[2024-03-26 19:10:21.015][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:21.017][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:21.020][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-26 19:10:21.427][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-26 19:10:21.827][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-03-26 19:10:21.830][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-03-26 19:10:21.832][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-03-26 19:10:21.837][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-03-26 19:10:21.842][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[2024-03-26 19:10:21.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:21.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:21.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-03-26 19:10:22.252][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-03-26 19:10:22.647][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:22.650][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-03-26 19:10:22.654][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-03-26 19:10:22.659][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:22.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:22.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:22.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:22.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:22.671][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:22.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:22.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:22.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:22.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:22.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:22.698][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:22.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:22.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:22.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:22.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:22.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:22.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:22.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:22.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:22.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:22.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:22.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:22.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:22.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:22.742][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-26 19:10:22.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:22.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:22.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:22.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:22.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:22.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:22.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:22.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.765][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.766][private$selectFields]
biodb.TRACE[2024-03-26 19:10:22.767][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:22.768][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:22.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.771][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.774][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.775][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.776][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.777][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.777][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.778][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.780][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.781][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.782][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.785][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.785][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:22.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.800][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-03-26 19:10:22.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:22.802][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:22.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:22.809][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:22.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:22.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:22.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:22.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.822][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.823][private$selectFields]
biodb.TRACE[2024-03-26 19:10:22.824][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:22.825][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:22.826][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.828][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.829][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.832][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.833][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.834][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.836][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.839][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.841][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.842][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.844][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.845][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.846][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:22.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.864][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-03-26 19:10:22.865][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:22.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:22.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:22.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:22.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:22.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:22.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:22.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.885][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.886][private$selectFields]
biodb.TRACE[2024-03-26 19:10:22.887][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-26 19:10:22.888][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-26 19:10:22.890][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.891][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.892][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.895][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.896][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.898][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.899][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.900][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.901][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.902][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-03-26 19:10:22.903][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.904][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.907][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.909][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-03-26 19:10:22.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:22.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:22.939][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-03-26 19:10:22.940][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-26 19:10:22.942][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-26 19:10:22.971][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:22.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-26 19:10:22.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:22.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-26 19:10:22.982][biodb::testThat]
biodb.INFO [2024-03-26 19:10:22.983][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2024-03-26 19:10:22.984][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:22.985][biodb::testThat]
biodb.DEBUG[2024-03-26 19:10:22.988][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-26 19:10:22.989][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:22.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-26 19:10:22.993][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:22.994][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:22.995][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:22.996][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:22.998][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:22.999][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:23.003][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:23.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:23.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:23.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:23.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:23.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:23.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:23.017][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-03-26 19:10:23.020][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:23.021][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:23.023][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-03-26 19:10:23.418][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-03-26 19:10:23.813][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:23.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-03-26 19:10:23.821][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-03-26 19:10:23.825][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-03-26 19:10:23.828][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:23.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:23.830][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:23.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:23.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:23.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:23.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:23.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:23.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:23.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:23.847][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.849][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.851][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.857][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:23.858][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:23.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.859][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.860][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:23.861][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:23.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.863][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.865][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:23.866][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:23.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.869][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.870][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:23.871][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:23.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.874][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:23.877][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:23.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.879][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.881][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:23.881][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:23.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.883][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.884][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:23.886][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:23.886][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.887][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.889][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:23.889][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:23.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.891][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.893][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:23.894][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:23.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.896][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.898][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:23.899][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:23.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.901][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:23.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:23.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:23.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:23.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:23.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:23.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:23.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:23.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:23.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:23.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:23.944][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-03-26 19:10:23.945][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-26 19:10:23.955][biodb::testThat]
biodb.INFO [2024-03-26 19:10:23.957][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-26 19:10:23.959][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:23.960][biodb::testThat]
biodb.DEBUG[2024-03-26 19:10:23.971][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-03-26 19:10:23.972][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-03-26 19:10:23.974][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-03-26 19:10:23.976][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-03-26 19:10:23.977][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-03-26 19:10:23.978][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:23.979][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:23.980][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:23.981][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:23.982][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:23.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:23.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:23.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:23.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:23.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:23.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:23.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:24.000][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-03-26 19:10:24.003][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:24.005][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:24.006][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-03-26 19:10:24.402][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-03-26 19:10:24.800][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-03-26 19:10:24.803][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-03-26 19:10:24.804][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-03-26 19:10:24.808][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-03-26 19:10:24.810][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:24.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:24.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:24.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:24.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:24.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:24.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:24.826][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-03-26 19:10:24.829][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:24.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:24.833][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-03-26 19:10:25.231][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-03-26 19:10:25.629][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:25.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-03-26 19:10:25.638][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-03-26 19:10:25.640][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:25.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:25.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:25.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:25.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:25.652][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:25.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:25.655][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-03-26 19:10:25.658][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:25.659][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:25.660][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-03-26 19:10:26.058][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-03-26 19:10:26.458][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:26.461][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-03-26 19:10:26.465][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-03-26 19:10:26.469][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-03-26 19:10:26.472][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:26.474][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-03-26 19:10:26.476][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:26.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:26.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:26.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:26.488][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:26.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:26.491][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:26.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:26.498][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.500][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.503][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.512][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:26.513][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:26.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.516][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.518][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:26.520][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:26.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.523][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.525][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:26.526][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:26.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.529][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.531][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.532][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.534][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.535][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.537][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.538][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.540][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.542][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:26.543][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:26.551][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.565][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.567][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.568][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.570][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.571][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:26.572][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:26.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.575][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.577][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:26.578][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:26.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.581][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.583][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:26.584][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:26.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.586][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.596][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:26.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:26.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:26.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:26.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:26.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:26.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:26.634][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[2024-03-26 19:10:26.637][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.638][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.640][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.646][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:26.648][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:26.649][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.650][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.652][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:26.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:26.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.657][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:26.658][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:26.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.661][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.663][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:26.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:26.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.669][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:26.670][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:26.672][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.673][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.675][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:26.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:26.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.680][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.681][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.684][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.689][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.690][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.693][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.694][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.699][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:26.700][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:26.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.703][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.704][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:26.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:26.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.711][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.713][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.715][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.722][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:26.723][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:26.724][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.726][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.728][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:26.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:26.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.734][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:26.735][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:26.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.737][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.738][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:26.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:26.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.742][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:26.743][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:26.744][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.744][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.746][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:26.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:26.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:26.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:26.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:26.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:26.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:26.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:26.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:26.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:26.825][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.826][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.828][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.829][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.838][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:26.839][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:26.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.842][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.844][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:26.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:26.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.848][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:26.849][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:26.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.851][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:26.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:26.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.857][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:26.859][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:26.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.860][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:26.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:26.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.866][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.867][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.869][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:26.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.875][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.876][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.878][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.880][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:26.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.885][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:26.887][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:26.888][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.889][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.891][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:26.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:26.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.896][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.897][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.899][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.900][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:26.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.905][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:26.906][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:26.907][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.908][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:26.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:26.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.916][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:26.917][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:26.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.920][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.921][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:26.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:26.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.925][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:26.926][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:26.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.927][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.928][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:26.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:26.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:26.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:26.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:26.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:26.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:26.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:27.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:27.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:27.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:27.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:27.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:27.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:27.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:27.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:27.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:27.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:27.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:27.013][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-03-26 19:10:27.014][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-26 19:10:27.015][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-03-26 19:10:27.031][biodb::testThat]
biodb.INFO [2024-03-26 19:10:27.032][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2024-03-26 19:10:27.033][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:27.034][biodb::testThat]
biodb.INFO [2024-03-26 19:10:27.067][biodb::testThat]
biodb.INFO [2024-03-26 19:10:27.068][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2024-03-26 19:10:27.069][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:27.070][biodb::testThat]
biodb.INFO [2024-03-26 19:10:27.083][biodb::testThat]
biodb.INFO [2024-03-26 19:10:27.084][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2024-03-26 19:10:27.086][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:27.087][biodb::testThat]
biodb.DEBUG[2024-03-26 19:10:27.090][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[2024-03-26 19:10:27.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:27.095][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:27.098][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-03-26 19:10:27.568][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-03-26 19:10:28.118][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:28.120][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-03-26 19:10:28.126][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-03-26 19:10:28.143][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:28.145][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:28.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:28.148][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:28.150][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:28.151][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:28.152][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:28.153][ef$get] fields variable is a list.
biodb.INFO [2024-03-26 19:10:28.155][biodb::testThat]
biodb.INFO [2024-03-26 19:10:28.156][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-26 19:10:28.158][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:28.159][biodb::testThat]
biodb.ERROR[2024-03-26 19:10:28.179][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-26 19:10:28.203][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-26 19:10:28.220][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-26 19:10:28.222][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-26 19:10:28.224][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-26 19:10:28.225][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-26 19:10:28.226][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.229][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.232][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-26 19:10:28.247][biodb::testContext]
biodb.INFO [2024-03-26 19:10:28.249][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:10:28.250][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-03-26 19:10:28.251][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:10:28.253][biodb::testContext]
biodb.INFO [2024-03-26 19:10:28.256][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:10:28.258][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-26 19:10:28.263][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:28.265][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-26 19:10:28.266][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-26 19:10:28.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.271][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-26 19:10:28.272][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-26 19:10:28.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.278][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-26 19:10:28.279][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-26 19:10:28.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.285][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-26 19:10:28.286][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-26 19:10:28.287][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-26 19:10:28.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.292][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-26 19:10:28.293][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-26 19:10:28.295][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-26 19:10:28.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.300][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-26 19:10:28.301][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-26 19:10:28.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.305][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-26 19:10:28.306][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-26 19:10:28.308][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-26 19:10:28.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.310][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[2024-03-26 19:10:28.311][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-26 19:10:28.312][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-26 19:10:28.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.317][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-26 19:10:28.319][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-26 19:10:28.321][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-26 19:10:28.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.326][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:10:28.328][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-26 19:10:28.329][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-26 19:10:28.331][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-26 19:10:28.332][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-26 19:10:28.333][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-26 19:10:28.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.338][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-26 19:10:28.339][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-26 19:10:28.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.344][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-26 19:10:28.345][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-26 19:10:28.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.350][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-26 19:10:28.351][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-26 19:10:28.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.356][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-26 19:10:28.357][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-26 19:10:28.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.362][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-26 19:10:28.363][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-26 19:10:28.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.368][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:10:28.369][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-26 19:10:28.397][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-26 19:10:28.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.402][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-26 19:10:28.402][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-26 19:10:28.403][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-26 19:10:28.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.406][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[2024-03-26 19:10:28.408][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-26 19:10:28.410][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.431][self$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[2024-03-26 19:10:28.433][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.434][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:28.436][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.437][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.439][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.440][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.442][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:10:28.443][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:28.444][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.445][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-26 19:10:28.446][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:28.447][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.448][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.449][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:28.449][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:28.449][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:28.449][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:10:28.449][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:10:28.449][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:28.451][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.452][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.453][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:28.454][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.454][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.455][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.456][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.458][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:28.459][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:28.460][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.461][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.463][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-26 19:10:28.465][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.466][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:10:28.466][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.467][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:28.468][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.469][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.470][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.484][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:10:28.486][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:28.487][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.489][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-26 19:10:28.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:28.492][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.493][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.495][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:28.495][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:28.495][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:28.495][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:10:28.495][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:10:28.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:28.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.500][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:28.501][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.503][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.505][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.506][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:28.507][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:28.508][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.509][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.510][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-26 19:10:28.512][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.513][self$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[2024-03-26 19:10:28.514][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.515][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:28.517][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.518][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.519][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.520][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.521][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:10:28.522][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:28.524][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.525][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-26 19:10:28.526][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:28.527][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.529][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.530][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.531][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:28.533][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.534][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.535][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:28.536][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.537][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.538][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.540][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.541][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:28.541][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:28.542][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.543][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.545][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-26 19:10:28.548][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.549][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:10:28.550][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.551][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:28.553][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.556][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.557][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.557][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:10:28.558][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:28.559][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.561][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-26 19:10:28.562][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:28.563][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.564][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.566][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.567][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:28.568][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.569][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.570][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:28.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:28.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:28.574][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.575][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.576][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:28.578][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:28.579][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.580][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:28.582][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:28.583][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.604][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.613][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.635][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.644][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.645][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.DEBUG[2024-03-26 19:10:28.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.650][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[2024-03-26 19:10:28.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.655][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[2024-03-26 19:10:28.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.661][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.671][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-26 19:10:28.673][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-26 19:10:28.675][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-26 19:10:28.677][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-26 19:10:28.679][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:10:28.681][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-26 19:10:28.682][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-26 19:10:28.684][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-26 19:10:28.685][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-26 19:10:28.687][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-26 19:10:28.689][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:10:28.691][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-26 19:10:28.693][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-26 19:10:28.695][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-26 19:10:28.697][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-26 19:10:28.699][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-26 19:10:28.701][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-26 19:10:28.703][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-26 19:10:28.704][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:10:28.705][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-26 19:10:28.707][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-26 19:10:28.708][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-26 19:10:28.710][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-26 19:10:28.712][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-26 19:10:28.713][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-26 19:10:28.714][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-26 19:10:28.716][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-26 19:10:28.718][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-26 19:10:28.720][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-26 19:10:28.721][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-26 19:10:28.722][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-26 19:10:28.724][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-26 19:10:28.726][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-26 19:10:28.728][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-26 19:10:28.730][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-26 19:10:28.731][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-26 19:10:28.733][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-26 19:10:28.735][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-26 19:10:28.737][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-26 19:10:28.739][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-26 19:10:28.741][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-26 19:10:28.743][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-26 19:10:28.744][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-26 19:10:28.747][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-26 19:10:28.749][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-26 19:10:28.752][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-26 19:10:28.755][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-26 19:10:28.758][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-26 19:10:28.760][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-26 19:10:28.763][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-26 19:10:28.764][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-26 19:10:28.766][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-26 19:10:28.768][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-26 19:10:28.770][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-26 19:10:28.771][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-26 19:10:28.772][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-26 19:10:28.774][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-26 19:10:28.776][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-26 19:10:28.777][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-26 19:10:28.778][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-26 19:10:28.780][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-26 19:10:28.782][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-26 19:10:28.783][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-26 19:10:28.784][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-26 19:10:28.786][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-26 19:10:28.787][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-26 19:10:28.789][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:10:28.791][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:10:28.793][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-26 19:10:28.794][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-26 19:10:28.796][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-26 19:10:28.798][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-26 19:10:28.800][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-26 19:10:28.802][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-26 19:10:28.804][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-26 19:10:28.806][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-26 19:10:28.807][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-26 19:10:28.810][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-26 19:10:28.811][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-26 19:10:28.813][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-26 19:10:28.815][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-26 19:10:28.816][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-26 19:10:28.817][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-26 19:10:28.818][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-26 19:10:28.820][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:10:28.822][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:28.823][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.825][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.836][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[2024-03-26 19:10:28.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.844][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.873][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.902][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[2024-03-26 19:10:28.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:28.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:28.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:28.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:28.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:28.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:28.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:28.972][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-26 19:10:28.986][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-26 19:10:28.989][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:28.991][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.993][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.994][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:28.995][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.996][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:28.997][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:28.998][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-26 19:10:29.000][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-26 19:10:29.001][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:29.002][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:29.003][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-26 19:10:29.004][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-26 19:10:29.006][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-26 19:10:29.007][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:29.008][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:29.008][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:29.008][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:29.010][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-26 19:10:29.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:29.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:29.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:29.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:29.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:29.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:29.018][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:29.018][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-26 19:10:29.020][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:29.021][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:29.022][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:29.023][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-26 19:10:29.023][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-26 19:10:29.025][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:10:29.027][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:10:29.030][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-26 19:10:29.031][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:10:29.034][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:10:29.035][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:10:29.040][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-26 19:10:29.042][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-26 19:10:29.044][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-26 19:10:29.046][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-26 19:10:29.048][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:10:29.049][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:10:29.051][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-26 19:10:29.053][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-26 19:10:29.055][biodb::testThat]
biodb.INFO [2024-03-26 19:10:29.056][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2024-03-26 19:10:29.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:29.059][biodb::testThat]
biodb.DEBUG[2024-03-26 19:10:29.063][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-26 19:10:29.067][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:29.069][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:29.070][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-03-26 19:10:29.481][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-03-26 19:10:30.057][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:30.059][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-03-26 19:10:30.064][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-03-26 19:10:30.069][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[2024-03-26 19:10:30.073][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:30.074][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:30.076][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-26 19:10:30.475][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-26 19:10:30.891][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:30.894][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-03-26 19:10:30.899][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-03-26 19:10:30.902][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:30.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:30.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:30.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:30.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:30.913][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:30.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:30.915][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-26 19:10:30.919][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:30.921][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:30.923][private$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[2024-03-26 19:10:31.340][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[2024-03-26 19:10:31.739][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:31.742][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-03-26 19:10:31.748][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-03-26 19:10:31.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:31.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:31.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:31.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:31.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:31.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:31.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:31.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:31.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:31.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:31.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:31.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:31.797][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:31.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:31.804][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[2024-03-26 19:10:31.808][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:31.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-03-26 19:10:31.813][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:31.815][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-03-26 19:10:31.818][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:31.819][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:31.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:31.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:31.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:31.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:31.831][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[2024-03-26 19:10:31.833][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[2024-03-26 19:10:31.839][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:31.841][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-03-26 19:10:31.843][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:31.845][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-03-26 19:10:31.847][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:31.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:31.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:31.857][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:31.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:31.860][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:31.861][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[2024-03-26 19:10:31.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:31.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:31.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:31.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:31.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:31.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:31.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:31.882][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[2024-03-26 19:10:31.886][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:31.887][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-03-26 19:10:31.889][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:31.891][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-03-26 19:10:31.893][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:31.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:31.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:31.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:31.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:31.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:31.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:31.924][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[2024-03-26 19:10:31.927][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:31.928][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-03-26 19:10:31.930][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:31.931][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-03-26 19:10:31.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:31.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:31.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:31.951][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:31.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:31.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:31.967][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[2024-03-26 19:10:31.969][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[2024-03-26 19:10:31.972][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:31.973][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:31.975][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-26 19:10:32.378][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-26 19:10:32.779][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:32.781][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-03-26 19:10:32.785][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-03-26 19:10:32.788][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:32.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:32.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:32.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:32.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:32.799][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:32.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-26 19:10:32.809][biodb::testThat]
biodb.INFO [2024-03-26 19:10:32.810][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2024-03-26 19:10:32.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:32.813][biodb::testThat]
biodb.DEBUG[2024-03-26 19:10:32.816][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-26 19:10:32.820][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:32.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:32.824][private$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[2024-03-26 19:10:33.222][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[2024-03-26 19:10:33.625][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:33.628][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-03-26 19:10:33.632][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-03-26 19:10:33.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:33.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:33.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:33.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:33.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:33.644][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:33.645][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.DEBUG[2024-03-26 19:10:33.651][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[2024-03-26 19:10:33.654][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:33.655][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:33.657][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-03-26 19:10:34.053][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-03-26 19:10:34.449][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:34.451][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-03-26 19:10:34.455][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-03-26 19:10:34.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:34.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:34.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:34.466][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-26 19:10:34.475][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-26 19:10:34.476][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-26 19:10:34.478][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-26 19:10:34.479][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-26 19:10:34.480][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:34.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:34.481][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.484][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-26 19:10:34.489][biodb::testContext]
biodb.INFO [2024-03-26 19:10:34.491][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:10:34.492][biodb::testContext] Test context - Test web services
biodb.INFO [2024-03-26 19:10:34.493][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:10:34.494][biodb::testContext]
biodb.INFO [2024-03-26 19:10:34.497][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:10:34.499][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-26 19:10:34.503][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:34.504][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-26 19:10:34.505][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-26 19:10:34.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.508][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-26 19:10:34.509][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-26 19:10:34.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.512][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-26 19:10:34.513][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-26 19:10:34.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.517][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-26 19:10:34.518][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-26 19:10:34.518][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-26 19:10:34.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.522][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-26 19:10:34.524][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-26 19:10:34.526][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-26 19:10:34.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.531][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-26 19:10:34.533][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-26 19:10:34.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.536][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-26 19:10:34.537][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-26 19:10:34.538][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-26 19:10:34.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.542][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-26 19:10:34.543][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-26 19:10:34.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.548][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-26 19:10:34.549][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-26 19:10:34.550][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-26 19:10:34.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.554][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:10:34.555][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-26 19:10:34.556][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-26 19:10:34.557][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-26 19:10:34.558][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-26 19:10:34.559][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-26 19:10:34.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.564][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-26 19:10:34.565][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-26 19:10:34.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.569][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-26 19:10:34.570][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-26 19:10:34.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.573][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-26 19:10:34.574][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-26 19:10:34.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.577][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-26 19:10:34.578][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-26 19:10:34.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.581][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-26 19:10:34.582][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-26 19:10:34.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.586][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:10:34.586][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-26 19:10:34.609][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-26 19:10:34.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.614][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-26 19:10:34.615][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-26 19:10:34.616][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-26 19:10:34.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.620][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-26 19:10:34.623][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.624][self$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[2024-03-26 19:10:34.625][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.626][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:34.627][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.628][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.630][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.631][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.632][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:10:34.633][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:34.634][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.635][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-26 19:10:34.637][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:34.638][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.639][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.640][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:34.640][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:34.640][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:34.640][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:10:34.640][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:10:34.641][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:34.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.642][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.644][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:34.646][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.648][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.650][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.651][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:34.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:34.654][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.656][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.657][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-26 19:10:34.658][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.659][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:10:34.660][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.661][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:34.662][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.663][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.664][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.665][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.666][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:10:34.667][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:34.668][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.669][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-26 19:10:34.670][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:34.671][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.672][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.673][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:34.673][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:34.673][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:34.673][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:10:34.673][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:10:34.674][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:34.675][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.678][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:34.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.680][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.681][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.682][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.683][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:34.683][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:34.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.685][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.686][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-26 19:10:34.688][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.689][self$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[2024-03-26 19:10:34.690][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.691][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:34.692][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.693][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.694][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.695][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.696][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:10:34.697][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:34.698][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.700][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-26 19:10:34.701][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:34.702][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.703][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.704][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.705][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:34.706][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.707][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.708][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:34.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.711][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.711][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.712][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:34.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:34.714][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.715][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.716][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-26 19:10:34.719][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.720][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:10:34.721][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.723][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:34.724][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.726][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.727][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.728][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.729][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:10:34.730][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:34.731][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.732][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-26 19:10:34.733][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:34.734][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.735][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:34.736][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.737][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:34.756][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.757][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.758][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:34.759][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:34.760][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:34.760][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:34.761][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.762][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:34.763][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:34.764][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:34.765][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:34.766][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:34.767][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.791][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.793][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.DEBUG[2024-03-26 19:10:34.794][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.810][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[2024-03-26 19:10:34.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.821][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[2024-03-26 19:10:34.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.831][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[2024-03-26 19:10:34.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.836][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[2024-03-26 19:10:34.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.847][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.855][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[2024-03-26 19:10:34.856][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-26 19:10:34.857][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-26 19:10:34.859][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-26 19:10:34.860][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-26 19:10:34.862][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:10:34.864][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-26 19:10:34.866][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-26 19:10:34.868][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-26 19:10:34.870][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-26 19:10:34.871][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-26 19:10:34.872][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:10:34.874][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-26 19:10:34.876][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-26 19:10:34.878][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-26 19:10:34.880][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-26 19:10:34.881][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-26 19:10:34.883][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-26 19:10:34.885][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-26 19:10:34.886][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:10:34.888][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-26 19:10:34.890][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-26 19:10:34.891][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-26 19:10:34.893][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-26 19:10:34.894][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-26 19:10:34.896][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-26 19:10:34.897][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-26 19:10:34.898][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-26 19:10:34.899][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-26 19:10:34.901][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-26 19:10:34.903][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-26 19:10:34.904][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-26 19:10:34.905][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-26 19:10:34.907][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-26 19:10:34.908][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-26 19:10:34.910][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-26 19:10:34.911][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-26 19:10:34.913][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-26 19:10:34.915][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-26 19:10:34.917][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-26 19:10:34.918][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-26 19:10:34.920][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-26 19:10:34.921][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-26 19:10:34.923][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-26 19:10:34.924][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-26 19:10:34.925][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-26 19:10:34.926][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-26 19:10:34.927][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-26 19:10:34.929][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-26 19:10:34.930][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-26 19:10:34.931][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-26 19:10:34.932][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-26 19:10:34.934][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-26 19:10:34.935][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-26 19:10:34.936][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-26 19:10:34.937][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-26 19:10:34.939][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-26 19:10:34.940][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-26 19:10:34.942][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-26 19:10:34.943][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-26 19:10:34.944][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-26 19:10:34.946][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-26 19:10:34.947][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-26 19:10:34.949][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-26 19:10:34.951][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-26 19:10:34.953][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-26 19:10:34.954][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-26 19:10:34.956][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:10:34.958][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:10:34.960][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-26 19:10:34.963][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-26 19:10:34.965][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-26 19:10:34.966][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-26 19:10:34.968][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-26 19:10:34.970][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-26 19:10:34.971][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-26 19:10:34.973][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-26 19:10:34.974][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-26 19:10:34.976][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-26 19:10:34.978][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-26 19:10:34.981][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-26 19:10:34.982][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-26 19:10:34.984][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-26 19:10:34.986][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-26 19:10:34.987][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-26 19:10:34.989][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:10:34.991][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:34.992][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:34.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:34.994][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:34.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:34.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:34.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:34.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.004][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[2024-03-26 19:10:35.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.025][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.037][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.DEBUG[2024-03-26 19:10:35.038][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.077][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.081][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[2024-03-26 19:10:35.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.087][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[2024-03-26 19:10:35.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:35.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:35.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:35.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:35.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:35.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:35.105][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-26 19:10:35.106][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-26 19:10:35.108][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:35.109][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-26 19:10:35.109][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:35.110][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:35.111][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:35.112][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:35.113][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:35.114][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-26 19:10:35.114][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-26 19:10:35.115][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:35.116][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:35.117][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-26 19:10:35.118][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-26 19:10:35.119][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-26 19:10:35.120][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:35.121][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:35.121][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:35.121][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:35.122][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-26 19:10:35.122][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:35.123][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:35.124][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:35.125][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:35.126][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:35.126][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:35.127][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:35.127][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-26 19:10:35.128][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:35.129][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:35.130][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:35.130][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-26 19:10:35.130][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-26 19:10:35.132][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:10:35.133][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:10:35.134][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-26 19:10:35.136][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:10:35.137][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:10:35.138][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:10:35.141][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-26 19:10:35.142][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-26 19:10:35.144][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-26 19:10:35.145][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-26 19:10:35.146][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:10:35.147][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:10:35.148][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-26 19:10:35.149][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-26 19:10:35.150][biodb::testThat]
biodb.INFO [2024-03-26 19:10:35.151][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-03-26 19:10:35.152][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:35.154][biodb::testThat]
biodb.DEBUG[2024-03-26 19:10:35.157][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-26 19:10:35.161][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:35.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-26 19:10:35.164][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:35.165][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-26 19:10:35.170][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-03-26 19:10:35.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:35.174][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:35.176][private$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[2024-03-26 19:10:35.572][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[2024-03-26 19:10:35.973][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:35.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-03-26 19:10:35.981][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-03-26 19:10:35.992][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-26 19:10:35.994][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-26 19:10:35.995][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-26 19:10:35.997][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-26 19:10:35.998][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:35.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.000][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.002][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.004][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.INFO [2024-03-26 19:10:36.008][biodb::testContext]
biodb.INFO [2024-03-26 19:10:36.009][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:10:36.010][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-03-26 19:10:36.011][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-26 19:10:36.012][biodb::testContext]
biodb.INFO [2024-03-26 19:10:36.015][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:10:36.016][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-26 19:10:36.021][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:36.023][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-26 19:10:36.024][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-26 19:10:36.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.029][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-26 19:10:36.030][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-26 19:10:36.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.033][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[2024-03-26 19:10:36.035][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-26 19:10:36.036][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-26 19:10:36.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.041][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-26 19:10:36.042][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-26 19:10:36.044][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-26 19:10:36.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.047][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-26 19:10:36.048][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-26 19:10:36.049][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-26 19:10:36.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.052][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-26 19:10:36.053][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-26 19:10:36.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.057][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-26 19:10:36.058][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-26 19:10:36.059][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-26 19:10:36.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.063][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-26 19:10:36.064][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-26 19:10:36.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.068][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-26 19:10:36.069][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-26 19:10:36.071][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-26 19:10:36.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.075][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:10:36.076][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-26 19:10:36.077][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-26 19:10:36.079][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-26 19:10:36.080][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-26 19:10:36.081][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-26 19:10:36.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.084][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-26 19:10:36.085][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-26 19:10:36.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.089][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-26 19:10:36.090][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-26 19:10:36.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.093][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-26 19:10:36.095][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-26 19:10:36.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.099][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-26 19:10:36.100][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-26 19:10:36.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.104][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-26 19:10:36.106][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-26 19:10:36.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.111][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-26 19:10:36.112][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-26 19:10:36.132][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-26 19:10:36.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.137][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-26 19:10:36.138][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-26 19:10:36.139][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-26 19:10:36.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.143][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-26 19:10:36.145][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.146][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-26 19:10:36.147][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.148][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:36.149][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.150][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.151][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.152][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.153][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:10:36.154][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:36.155][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.156][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-26 19:10:36.156][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:36.157][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.158][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.159][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:36.159][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:36.159][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:36.159][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:10:36.159][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:10:36.160][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:36.161][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.163][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:36.163][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.164][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.165][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.166][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.167][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:36.168][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:36.168][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.169][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.170][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-26 19:10:36.172][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.173][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:10:36.174][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.175][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:36.176][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.176][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.177][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.178][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.179][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:10:36.180][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:36.181][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.182][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-26 19:10:36.183][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:36.184][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.184][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.185][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:36.185][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:36.185][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:36.185][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-26 19:10:36.185][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-26 19:10:36.186][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:36.187][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.188][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.189][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:36.191][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.192][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.193][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.194][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.195][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:36.196][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:36.196][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.197][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.198][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-26 19:10:36.201][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.202][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-26 19:10:36.203][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.205][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:36.206][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.207][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.209][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.210][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.211][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-26 19:10:36.212][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:36.213][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.215][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-26 19:10:36.216][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:36.217][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.218][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.220][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.221][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:36.222][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.223][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.224][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:36.225][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.226][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.228][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.229][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.230][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:36.231][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:36.233][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.234][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.235][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-26 19:10:36.237][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.238][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-26 19:10:36.239][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.240][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:36.241][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.243][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.244][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.245][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.246][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-26 19:10:36.247][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:36.249][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.250][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-26 19:10:36.251][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:36.252][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.253][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.255][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.256][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-26 19:10:36.257][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.258][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.259][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:36.268][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.273][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.275][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.276][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.277][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:36.278][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:36.279][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.280][self$setPropertyValue]
biodb.DEBUG[2024-03-26 19:10:36.281][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:36.282][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.310][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[2024-03-26 19:10:36.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.319][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[2024-03-26 19:10:36.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.338][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[2024-03-26 19:10:36.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.354][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[2024-03-26 19:10:36.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.359][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-26 19:10:36.360][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-26 19:10:36.362][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-26 19:10:36.363][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-26 19:10:36.364][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:10:36.366][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-26 19:10:36.367][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-26 19:10:36.368][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-26 19:10:36.369][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-26 19:10:36.370][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-26 19:10:36.372][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:10:36.373][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-26 19:10:36.374][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-26 19:10:36.375][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-26 19:10:36.376][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-26 19:10:36.377][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-26 19:10:36.378][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-26 19:10:36.380][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-26 19:10:36.381][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:10:36.382][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-26 19:10:36.383][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-26 19:10:36.384][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-26 19:10:36.385][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-26 19:10:36.387][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-26 19:10:36.388][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-26 19:10:36.389][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-26 19:10:36.390][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-26 19:10:36.391][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-26 19:10:36.392][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-26 19:10:36.394][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-26 19:10:36.395][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-26 19:10:36.396][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-26 19:10:36.397][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-26 19:10:36.398][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-26 19:10:36.400][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-26 19:10:36.401][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-26 19:10:36.402][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-26 19:10:36.403][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-26 19:10:36.404][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-26 19:10:36.405][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-26 19:10:36.406][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-26 19:10:36.408][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-26 19:10:36.409][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-26 19:10:36.410][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-26 19:10:36.411][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-26 19:10:36.412][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-26 19:10:36.414][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-26 19:10:36.415][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-26 19:10:36.416][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-26 19:10:36.418][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-26 19:10:36.420][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-26 19:10:36.422][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-26 19:10:36.423][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-26 19:10:36.424][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-26 19:10:36.426][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-26 19:10:36.427][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-26 19:10:36.428][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-26 19:10:36.429][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-26 19:10:36.430][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-26 19:10:36.432][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-26 19:10:36.433][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-26 19:10:36.434][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-26 19:10:36.435][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-26 19:10:36.436][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-26 19:10:36.438][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-26 19:10:36.439][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-26 19:10:36.440][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:10:36.441][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:10:36.442][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-26 19:10:36.444][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-26 19:10:36.445][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-26 19:10:36.446][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-26 19:10:36.447][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-26 19:10:36.448][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-26 19:10:36.450][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-26 19:10:36.451][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-26 19:10:36.452][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-26 19:10:36.453][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-26 19:10:36.454][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-26 19:10:36.456][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-26 19:10:36.457][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-26 19:10:36.458][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-26 19:10:36.459][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-26 19:10:36.460][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-26 19:10:36.462][initialize] This is biodb version 1.11.0.
biodb.DEBUG[2024-03-26 19:10:36.463][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-26 19:10:36.464][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.465][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.466][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[2024-03-26 19:10:36.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.472][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[2024-03-26 19:10:36.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.488][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[2024-03-26 19:10:36.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.494][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[2024-03-26 19:10:36.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.531][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-26 19:10:36.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.587][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-03-26 19:10:36.589][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-03-26 19:10:36.591][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.592][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.594][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.595][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-26 19:10:36.596][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.598][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.599][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.600][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-03-26 19:10:36.601][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-03-26 19:10:36.602][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-26 19:10:36.603][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.605][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-03-26 19:10:36.606][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-03-26 19:10:36.608][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-03-26 19:10:36.609][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-26 19:10:36.611][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-26 19:10:36.611][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-26 19:10:36.611][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-26 19:10:36.612][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-03-26 19:10:36.613][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.615][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-26 19:10:36.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-26 19:10:36.617][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-26 19:10:36.618][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-26 19:10:36.619][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:36.619][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-03-26 19:10:36.620][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-26 19:10:36.621][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-26 19:10:36.621][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-26 19:10:36.622][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-03-26 19:10:36.622][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-03-26 19:10:36.624][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-26 19:10:36.626][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-26 19:10:36.628][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-03-26 19:10:36.629][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-26 19:10:36.630][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-26 19:10:36.632][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-26 19:10:36.636][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-03-26 19:10:36.637][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-03-26 19:10:36.639][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-03-26 19:10:36.640][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-03-26 19:10:36.642][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:10:36.643][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-03-26 19:10:36.644][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-03-26 19:10:36.645][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-03-26 19:10:36.647][biodb::testThat]
biodb.INFO [2024-03-26 19:10:36.648][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-03-26 19:10:36.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-26 19:10:36.650][biodb::testThat]
biodb.DEBUG[2024-03-26 19:10:36.653][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-03-26 19:10:36.658][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:36.659][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-03-26 19:10:36.661][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:36.663][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-03-26 19:10:36.666][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[2024-03-26 19:10:36.669][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-26 19:10:36.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-03-26 19:10:36.672][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-26 19:10:36.673][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-03-26 19:10:36.694][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-03-26 19:10:36.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-26 19:10:36.698][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-03-26 19:10:36.700][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-26 19:10:36.701][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-26 19:10:36.702][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-03-26 19:10:36.704][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-03-26 19:10:36.705][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-26 19:10:36.706][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-26 19:10:36.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:36.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:36.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:36.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:36.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:36.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:36.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-26 19:10:36.721][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-03-26 19:10:36.724][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-26 19:10:36.724][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-26 19:10:36.726][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-03-26 19:10:37.129][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-03-26 19:10:38.367][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-26 19:10:38.370][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-03-26 19:10:38.377][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-03-26 19:10:38.381][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-03-26 19:10:38.385][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-26 19:10:38.388][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-03-26 19:10:38.389][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-03-26 19:10:38.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-26 19:10:38.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:38.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:38.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:38.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:38.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:38.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-26 19:10:38.414][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.415][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.418][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.427][ef$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:38.429][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:38.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.432][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.434][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-03-26 19:10:38.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-03-26 19:10:38.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.440][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:38.441][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:38.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.444][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.445][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-26 19:10:38.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-26 19:10:38.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.452][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-03-26 19:10:38.454][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-03-26 19:10:38.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.456][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.458][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-03-26 19:10:38.460][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-03-26 19:10:38.461][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.462][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.464][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:38.466][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:38.467][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.469][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.471][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:38.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-26 19:10:38.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.476][ef$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:38.478][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:38.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.481][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.483][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-03-26 19:10:38.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-26 19:10:38.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:38.491][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:38.492][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.494][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.496][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:38.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-26 19:10:38.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.502][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:38.503][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:38.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.507][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-26 19:10:38.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-26 19:10:38.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.516][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:38.518][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:38.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.521][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.523][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-03-26 19:10:38.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-03-26 19:10:38.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.529][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:38.530][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:38.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.533][ef$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.535][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-03-26 19:10:38.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-03-26 19:10:38.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:38.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:38.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:38.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:38.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-26 19:10:38.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-26 19:10:38.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-26 19:10:38.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-26 19:10:38.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-26 19:10:38.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-26 19:10:38.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-26 19:10:38.609][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-03-26 19:10:38.618][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-26 19:10:38.620][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-03-26 19:10:38.626][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-03-26 19:10:38.628][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-26 19:10:38.629][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-26 19:10:38.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-26 19:10:38.633][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-26 19:10:38.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-26 19:10:38.635][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-26 19:10:38.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 384 ]
> 
> proc.time()
   user  system elapsed 
 22.442   1.561  56.818 

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

nameusersystemelapsed
ChebiConn2.9431.0925.466
ChebiEntry0.4960.0250.540