Multiple platform build/check report for BioC 3.21 - CHECK results for biodbChebi on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"	4783
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4552
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4581
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4533
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4463
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for biodbChebi on palomino7

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: 1.13.0

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbChebi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings biodbChebi_1.13.0.tar.gz

StartedAt: 2025-03-26 23:36:44 -0400 (Wed, 26 Mar 2025)

EndedAt: 2025-03-26 23:41:46 -0400 (Wed, 26 Mar 2025)

EllapsedTime: 301.4 seconds

RetCode: 0

Status: OK

CheckDir: biodbChebi.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbChebi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings biodbChebi_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck'
* using R Under development (unstable) (2025-03-01 r87860 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biodbChebi/DESCRIPTION' ... OK
* this is package 'biodbChebi' version '1.13.0'
* 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 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 4.18   2.25  152.14
* 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:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL biodbChebi
###
##############################################################################
##############################################################################


* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'biodbChebi' ...
** this is package 'biodbChebi' version '1.13.0'
** 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) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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 [2025-03-26 23:40:39.419][biodb::testContext]
biodb.INFO [2025-03-26 23:40:39.422][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:40:39.424][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-26 23:40:39.425][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:40:39.427][biodb::testContext]
biodb.INFO [2025-03-26 23:40:39.434][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:40:39.437][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 23:40:39.447][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:40:39.449][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 23:40:39.450][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 23:40:39.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.455][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 23:40:39.502][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 23:40:39.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.510][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 23:40:39.512][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 23:40:39.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.518][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 23:40:39.519][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 23:40:39.520][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 23:40:39.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.525][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 23:40:39.526][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 23:40:39.527][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 23:40:39.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.531][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 23:40:39.533][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 23:40:39.534][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.537][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 23:40:39.538][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 23:40:39.540][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 23:40:39.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.547][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 23:40:39.549][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 23:40:39.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.556][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 23:40:39.558][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 23:40:39.560][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 23:40:39.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.563][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.567][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:40:39.568][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 23:40:39.570][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 23:40:39.572][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 23:40:39.574][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 23:40:39.576][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 23:40:39.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.581][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[2025-03-26 23:40:39.583][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 23:40:39.585][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 23:40:39.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.592][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 23:40:39.594][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 23:40:39.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.601][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 23:40:39.603][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 23:40:39.605][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.610][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 23:40:39.612][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 23:40:39.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.617][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[2025-03-26 23:40:39.618][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 23:40:39.620][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 23:40:39.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.623][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.624][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:40:39.626][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 23:40:39.629][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 23:40:39.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.634][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 23:40:39.635][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 23:40:39.636][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 23:40:39.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.645][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 23:40:39.677][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.691][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 23:40:39.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.694][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:40:39.695][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.698][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.699][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.700][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:40:39.701][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:40:39.703][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.704][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 23:40:39.705][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:40:39.707][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.708][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.709][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:40:39.709][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:40:39.709][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:40:39.709][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:40:39.709][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:40:39.716][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:40:39.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.719][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.720][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:40:39.721][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.722][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.724][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.725][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.726][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:40:39.727][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:40:39.728][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.729][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.731][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 23:40:39.733][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.734][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:40:39.735][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.736][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:40:39.737][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.739][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.740][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.741][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.742][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:40:39.744][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:40:39.745][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.746][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 23:40:39.747][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:40:39.749][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.750][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.751][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:40:39.751][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:40:39.751][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:40:39.751][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:40:39.751][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:40:39.752][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:40:39.754][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.755][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.756][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:40:39.757][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.758][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.760][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.762][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.764][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:40:39.765][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:40:39.766][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.767][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.769][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 23:40:39.771][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.772][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 23:40:39.773][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.774][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:40:39.775][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.777][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.778][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.779][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.780][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:40:39.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:40:39.782][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.784][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 23:40:39.785][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:40:39.786][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.787][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.788][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.790][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:40:39.791][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.792][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.793][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:40:39.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.796][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.798][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:40:39.800][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:40:39.801][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.802][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.804][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 23:40:39.806][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.807][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:40:39.808][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.809][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:40:39.810][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.812][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.813][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.814][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.815][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:40:39.816][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:40:39.818][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.819][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 23:40:39.820][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:40:39.821][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.822][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:39.824][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.825][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:40:39.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.828][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:40:39.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:39.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:39.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:40:39.833][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:40:39.835][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:40:39.836][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:39.837][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:40:39.841][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:40:39.842][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.854][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[2025-03-26 23:40:39.856][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.858][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.865][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.DEBUG[2025-03-26 23:40:39.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.871][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[2025-03-26 23:40:39.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.876][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[2025-03-26 23:40:39.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.893][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[2025-03-26 23:40:39.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.916][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:39.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:39.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:39.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:39.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:39.957][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[2025-03-26 23:40:39.959][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 23:40:39.965][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 23:40:39.968][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 23:40:39.970][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 23:40:39.973][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:40:39.975][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 23:40:39.978][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 23:40:39.980][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 23:40:39.983][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 23:40:39.985][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 23:40:39.988][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:40:39.990][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 23:40:39.992][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 23:40:39.994][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 23:40:39.996][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 23:40:39.998][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 23:40:39.999][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 23:40:40.001][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 23:40:40.002][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:40:40.004][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 23:40:40.005][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 23:40:40.007][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 23:40:40.009][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 23:40:40.010][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 23:40:40.012][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 23:40:40.013][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 23:40:40.015][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 23:40:40.016][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 23:40:40.018][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 23:40:40.019][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 23:40:40.021][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 23:40:40.022][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 23:40:40.024][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 23:40:40.026][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 23:40:40.027][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 23:40:40.029][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 23:40:40.030][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 23:40:40.032][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 23:40:40.033][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 23:40:40.035][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 23:40:40.037][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 23:40:40.038][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 23:40:40.040][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 23:40:40.042][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 23:40:40.043][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 23:40:40.045][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 23:40:40.046][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 23:40:40.048][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 23:40:40.050][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 23:40:40.051][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 23:40:40.053][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 23:40:40.054][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 23:40:40.056][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 23:40:40.058][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 23:40:40.060][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 23:40:40.062][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 23:40:40.064][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 23:40:40.065][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 23:40:40.067][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 23:40:40.068][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 23:40:40.070][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 23:40:40.072][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 23:40:40.073][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 23:40:40.075][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 23:40:40.076][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 23:40:40.078][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 23:40:40.079][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:40:40.081][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:40:40.082][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 23:40:40.084][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 23:40:40.086][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 23:40:40.087][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 23:40:40.089][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 23:40:40.091][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 23:40:40.093][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 23:40:40.094][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 23:40:40.096][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 23:40:40.097][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 23:40:40.099][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 23:40:40.100][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 23:40:40.102][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 23:40:40.104][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 23:40:40.106][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 23:40:40.142][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 23:40:40.146][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:40:40.151][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:40:40.153][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.156][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.177][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.229][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[2025-03-26 23:40:40.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.235][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.253][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.276][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.290][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[2025-03-26 23:40:40.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.298][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:40:40.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:40.315][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 23:40:40.324][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 23:40:40.326][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:40.327][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 23:40:40.328][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:40.330][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:40:40.331][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:40.332][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:40:40.333][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:40.334][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 23:40:40.335][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 23:40:40.337][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:40:40.338][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:40.339][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 23:40:40.340][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 23:40:40.341][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 23:40:40.343][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 23:40:40.344][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:40:40.344][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:40:40.344][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:40:40.345][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 23:40:40.346][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:40.347][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:40.348][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:40:40.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:40:40.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:40:40.352][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:40:40.353][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:40.353][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 23:40:40.354][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:40:40.355][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:40:40.356][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 23:40:40.358][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 23:40:40.358][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 23:40:40.363][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:40:40.365][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:40:40.367][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 23:40:40.368][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:40:40.371][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:40:40.373][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:40:40.402][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 23:40:40.403][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 23:40:40.408][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 23:40:40.412][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 23:40:40.416][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:40:40.417][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:40:40.419][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 23:40:40.420][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 23:40:40.475][biodb::testThat]
biodb.INFO [2025-03-26 23:40:40.477][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-26 23:40:40.479][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:40.481][biodb::testThat]
biodb.TRACE[2025-03-26 23:40:40.516][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-26 23:40:40.519][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:40.522][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:40.532][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:40.534][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:40.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:40.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:40.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:40.561][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:40.562][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[2025-03-26 23:40:40.572][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.574][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.576][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.577][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.594][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:40.595][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:40.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.622][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:40.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:40.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.631][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:40.633][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:40.634][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.635][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.637][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:40.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:40.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.641][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:40.643][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:40.644][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.645][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.646][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:40.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:40.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.651][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.653][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.654][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.655][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.661][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:40.663][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:40.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.665][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.666][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:40.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:40.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.671][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:40.673][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:40.674][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.675][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.677][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:40.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:40.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.684][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:40.686][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:40.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:40.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:40.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.700][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:40.702][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:40.704][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.716][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:40.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:40.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.722][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:40.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:40.725][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.726][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.727][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:40.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:40.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.732][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:40.734][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:40.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.736][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.737][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:40.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:40.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:40.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:40.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:40.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:40.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:40.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:40.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:40.834][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-26 23:40:40.839][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:40.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:40.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:40.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:40.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:40.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:40.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:40.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.920][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:40.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:40.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.928][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 23:40:40.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 23:40:40.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.936][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 23:40:40.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 23:40:40.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.942][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 23:40:40.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 23:40:40.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 23:40:40.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 23:40:40.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:40.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:40.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:40.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:40.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.270][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.272][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.273][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.274][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.331][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.338][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.339][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.341][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:41.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.367][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:41.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:41.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:41.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:41.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:41.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:41.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.392][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:41.394][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:41.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.397][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:41.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:41.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.416][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:41.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:41.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.423][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:41.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:41.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.431][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:41.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:41.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.439][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:41.441][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:41.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.445][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:41.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:41.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.489][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.491][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.494][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.545][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.547][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.549][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.578][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:41.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:41.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.585][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:41.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:41.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.590][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:41.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:41.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.595][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:41.596][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:41.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.598][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.600][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:41.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:41.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.627][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.636][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.650][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.651][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.653][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.655][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.675][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.680][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.686][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.690][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.692][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.693][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.695][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.714][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:41.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:41.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.720][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:41.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:41.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.725][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:41.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:41.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.729][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:41.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:41.732][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.733][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.734][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:41.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:41.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.754][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.773][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.775][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.777][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:41.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:41.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:41.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:41.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.809][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:41.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:41.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.813][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:41.815][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:41.816][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.817][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:41.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:41.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.838][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:41.841][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:41.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.865][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:41.867][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:41.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.870][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.890][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:41.892][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:41.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.897][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.911][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:41.913][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:41.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.925][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.927][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:41.928][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.929][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.938][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.939][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:41.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.942][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.949][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.950][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:41.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.953][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.960][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.962][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:41.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.974][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.976][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:41.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.988][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:41.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:41.990][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:41.991][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:41.999][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:42.001][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:42.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.005][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 23:40:42.028][biodb::testThat]
biodb.INFO [2025-03-26 23:40:42.029][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-26 23:40:42.030][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:42.031][biodb::testThat]
biodb.DEBUG[2025-03-26 23:40:42.049][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-26 23:40:42.056][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:42.063][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-26 23:40:42.064][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:42.067][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-26 23:40:42.069][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:42.089][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:42.091][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:42.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:42.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:42.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:42.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:42.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:42.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:42.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:42.109][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.110][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.111][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.133][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:42.134][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:42.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.138][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:42.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:42.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.143][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:42.144][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:42.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.148][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:42.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:42.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.153][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:42.154][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:42.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.156][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:42.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:42.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.162][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.164][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.165][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.166][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.167][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.172][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:42.173][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:42.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.176][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.177][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:42.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:42.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.182][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:42.183][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.184][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.187][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:42.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:42.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:42.200][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.201][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:42.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:42.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.208][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.209][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.218][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:42.219][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:42.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.221][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.223][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:42.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:42.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.228][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:42.229][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:42.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.233][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:42.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:42.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:42.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:42.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:42.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:42.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:42.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:42.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:42.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:42.287][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-26 23:40:42.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-26 23:40:42.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-26 23:40:42.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-26 23:40:42.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-26 23:40:42.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-26 23:40:42.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-26 23:40:42.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 23:40:42.315][biodb::testThat]
biodb.INFO [2025-03-26 23:40:42.317][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-26 23:40:42.319][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:42.321][biodb::testThat]
biodb.TRACE[2025-03-26 23:40:42.326][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.328][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.332][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:42.335][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-26 23:40:42.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.406][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:42.413][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-26 23:40:42.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 23:40:42.437][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:42.458][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-26 23:40:42.460][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:42.463][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-26 23:40:42.490][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[2025-03-26 23:40:42.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:42.497][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 23:40:42.499][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:42.554][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 23:40:42.557][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-26 23:40:42.588][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:42.589][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:42.591][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.592][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.594][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.595][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.596][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.597][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 23:40:42.611][biodb::testThat]
biodb.INFO [2025-03-26 23:40:42.613][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-26 23:40:42.615][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:42.617][biodb::testThat]
biodb.TRACE[2025-03-26 23:40:42.673][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.680][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:42.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:42.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:42.758][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[2025-03-26 23:40:42.762][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:42.764][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 23:40:42.766][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:42.768][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-26 23:40:42.809][biodb::testThat]
biodb.INFO [2025-03-26 23:40:42.811][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-26 23:40:42.812][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:42.813][biodb::testThat]
biodb.TRACE[2025-03-26 23:40:42.841][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:42.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:42.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.846][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:42.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:42.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.861][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.870][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.875][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.880][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 23:40:42.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 23:40:42.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.885][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 23:40:42.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 23:40:42.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:42.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:42.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:42.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:42.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.914][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:42.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:42.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.933][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.939][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-26 23:40:42.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.947][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-26 23:40:42.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-26 23:40:42.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:42.955][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-26 23:40:42.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-26 23:40:42.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:42.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 23:40:42.981][biodb::testThat]
biodb.INFO [2025-03-26 23:40:42.983][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-26 23:40:42.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:42.993][biodb::testThat]
biodb.INFO [2025-03-26 23:40:43.011][biodb::testThat]
biodb.INFO [2025-03-26 23:40:43.012][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-26 23:40:43.014][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:43.015][biodb::testThat]
biodb.INFO [2025-03-26 23:40:43.030][biodb::testThat]
biodb.INFO [2025-03-26 23:40:43.032][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-26 23:40:43.033][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:43.034][biodb::testThat]
biodb.DEBUG[2025-03-26 23:40:43.039][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-26 23:40:43.796][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-26 23:40:44.450][biodb::testThat]
biodb.INFO [2025-03-26 23:40:44.452][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-26 23:40:44.453][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:44.454][biodb::testThat]
biodb.DEBUG[2025-03-26 23:40:44.755][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[2025-03-26 23:40:45.081][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:45.083][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:45.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.087][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.089][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:45.091][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:45.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.095][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 23:40:45.097][biodb::testThat]
biodb.INFO [2025-03-26 23:40:45.098][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-03-26 23:40:45.100][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:40:45.101][biodb::testThat]
biodb.TRACE[2025-03-26 23:40:45.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:45.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:45.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:45.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:45.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.144][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:45.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:45.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:45.330][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[2025-03-26 23:40:45.334][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:45.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 23:40:45.340][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:45.342][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 23:40:45.464][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[2025-03-26 23:40:45.471][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:45.473][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 23:40:45.474][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:45.478][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-26 23:40:45.514][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 23:40:45.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 23:40:45.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:45.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:45.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:45.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:45.583][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[2025-03-26 23:40:45.589][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:45.591][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-26 23:40:45.593][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:45.607][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-26 23:40:45.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:45.611][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:45.612][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:45.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:45.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:45.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:45.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:45.640][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-26 23:40:45.683][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:45.685][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-26 23:40:45.687][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:45.688][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:45.690][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:45.691][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:45.692][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:45.694][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:45.706][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:45.708][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:45.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:45.717][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:45.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:45.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:45.720][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[2025-03-26 23:40:45.722][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-26 23:40:45.726][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:45.727][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:45.728][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-26 23:40:46.007][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-26 23:40:46.299][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:46.303][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-26 23:40:46.320][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-26 23:40:46.324][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-26 23:40:46.327][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:46.329][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:46.330][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:46.332][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:46.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:46.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:46.349][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:46.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:46.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:46.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:46.356][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.357][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.358][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.360][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.366][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:46.368][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:46.369][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.372][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:46.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:46.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.377][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:46.378][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:46.379][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.380][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.382][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:46.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:46.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.387][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:46.389][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:46.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.393][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:46.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:46.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.406][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:46.407][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:46.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.410][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:46.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:46.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.417][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:46.418][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:46.419][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.420][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.422][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:46.423][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.425][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.427][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:46.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.432][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:46.433][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:46.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.436][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:46.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:46.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.442][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:46.444][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:46.445][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:46.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:46.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.453][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:46.454][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:46.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.457][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.458][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:46.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:46.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.463][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:46.464][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:46.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.468][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:46.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:46.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:46.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:46.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:46.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:46.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.494][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:46.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:46.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:46.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:46.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:46.561][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-26 23:40:46.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.581][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:46.587][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[2025-03-26 23:40:46.591][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:46.592][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-26 23:40:46.594][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:46.625][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-26 23:40:46.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:46.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:46.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:46.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:46.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:46.670][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:46.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:46.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:46.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:46.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:46.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:46.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:46.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:46.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:46.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:46.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:46.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:46.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:46.716][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-26 23:40:46.718][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:46.720][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-26 23:40:46.722][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:46.724][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:46.725][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:46.727][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:46.729][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:46.731][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:46.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:46.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:46.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:46.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:46.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:46.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:46.774][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.DEBUG[2025-03-26 23:40:46.776][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-26 23:40:46.790][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:46.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:46.816][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-26 23:40:47.100][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-26 23:40:47.381][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:47.384][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-26 23:40:47.390][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-26 23:40:47.395][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-26 23:40:47.398][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:47.406][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:47.410][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:47.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:47.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:47.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:47.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:47.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:47.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:47.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:47.431][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.433][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.435][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.437][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.444][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:47.445][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:47.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.448][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.449][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:47.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:47.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.455][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:47.456][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:47.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.460][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:47.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:47.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.466][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:47.467][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:47.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.471][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:47.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:47.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.478][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:47.480][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:47.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:47.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:47.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.491][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:47.493][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:47.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.499][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:47.500][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.503][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.505][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:47.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.510][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:47.512][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:47.514][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:47.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:47.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.522][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:47.523][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:47.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.527][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:47.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:47.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.533][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:47.535][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:47.536][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.537][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.539][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:47.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:47.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.550][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:47.552][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:47.553][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:47.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:47.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:47.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:47.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:47.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.576][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:47.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:47.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:47.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:47.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:47.624][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-26 23:40:47.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:47.700][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[2025-03-26 23:40:47.706][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:40:47.709][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 23:40:47.712][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:40:47.716][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 23:40:47.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:47.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:47.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:47.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:47.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:47.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:47.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:47.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:47.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:47.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:47.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:47.767][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:47.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:47.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:47.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:47.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:47.780][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:47.781][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[2025-03-26 23:40:47.783][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-26 23:40:47.784][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:47.786][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-26 23:40:47.788][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:47.789][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:47.790][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:47.792][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:47.793][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:47.794][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:47.797][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:47.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:47.799][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:47.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:47.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:47.821][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:47.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:47.824][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-26 23:40:47.827][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:47.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:47.829][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-26 23:40:48.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-26 23:40:48.390][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:48.393][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-26 23:40:48.398][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-26 23:40:48.401][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-26 23:40:48.403][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:48.405][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:48.407][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:48.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:48.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:48.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:48.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:48.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:48.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:48.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:48.448][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.449][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.451][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.452][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.466][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:48.468][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:48.470][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.471][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.473][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:48.474][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:48.475][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.477][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.478][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:48.480][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:48.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.482][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.484][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:48.485][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:48.487][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.488][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.489][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:48.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:48.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.493][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.495][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:48.496][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:48.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:48.502][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.504][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.505][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:48.506][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:48.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.509][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.510][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:48.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:48.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.516][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:48.517][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:48.518][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.519][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.521][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:48.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:48.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.526][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:48.527][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:48.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:48.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:48.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:48.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:48.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:48.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:48.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:48.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:48.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:48.609][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-26 23:40:48.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:48.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:48.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:48.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:48.636][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:48.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:48.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:48.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:48.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:48.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:48.655][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[2025-03-26 23:40:48.657][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-26 23:40:48.659][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:48.661][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-26 23:40:48.663][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:48.665][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:48.666][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:48.667][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:48.669][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:48.670][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:48.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:48.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:48.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:48.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:48.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:48.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:48.697][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[2025-03-26 23:40:48.700][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-26 23:40:48.705][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:48.707][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:48.708][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-26 23:40:48.992][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-26 23:40:49.274][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:49.277][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-26 23:40:49.282][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-26 23:40:49.286][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-26 23:40:49.288][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:49.289][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:49.291][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:49.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:49.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:49.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:49.309][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:49.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:49.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:49.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:49.316][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.318][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.319][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.327][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.335][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:49.336][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:49.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.340][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:49.341][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:49.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.345][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:49.346][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:49.348][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.349][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.350][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:49.352][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:49.353][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.354][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.356][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:49.358][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:49.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.364][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:49.366][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.368][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.370][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.372][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:49.373][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:49.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.376][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.379][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:49.381][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:49.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.385][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:49.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:49.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.395][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:49.396][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:49.397][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.398][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.400][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:49.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.405][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:49.406][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:49.407][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.409][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:49.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:49.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:49.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:49.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:49.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:49.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:49.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:49.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:49.488][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-26 23:40:49.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:49.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:49.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:49.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:49.525][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:49.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:49.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:49.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:49.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:49.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:49.543][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:49.544][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-26 23:40:49.546][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:49.547][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-26 23:40:49.549][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:49.551][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:49.552][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:49.553][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:49.554][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:49.555][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:49.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:49.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:49.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:49.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:49.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:49.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:49.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:49.581][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-26 23:40:49.584][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:49.585][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:49.587][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-26 23:40:49.868][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-26 23:40:50.149][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:50.154][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-26 23:40:50.159][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-26 23:40:50.164][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-26 23:40:50.166][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:50.168][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:50.169][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:50.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:50.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:50.174][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:50.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:50.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:50.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:50.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:50.203][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.204][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.207][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.213][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:50.215][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:50.216][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.217][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.218][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:50.220][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:50.221][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.222][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.224][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:50.225][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:50.226][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.227][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.229][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:50.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:50.231][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.232][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.234][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:50.235][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:50.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.238][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.239][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:50.240][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.242][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.244][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:50.245][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:50.247][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.248][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.249][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:50.250][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:50.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.253][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.255][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:50.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.260][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:50.261][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:50.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.265][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:50.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:50.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.271][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:50.273][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:50.275][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.277][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:50.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:50.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:50.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:50.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:50.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:50.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:50.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:50.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:50.357][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-26 23:40:50.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:50.390][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:50.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:50.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:50.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:50.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:50.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:50.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:50.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:50.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:50.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:50.409][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-26 23:40:50.411][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:50.413][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-26 23:40:50.414][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:50.416][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:50.417][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:50.418][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:50.419][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:50.421][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:50.423][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:50.424][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:50.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:50.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:50.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:50.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:50.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:50.443][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-26 23:40:50.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:50.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:50.449][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-26 23:40:50.732][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-26 23:40:51.030][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:51.032][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-26 23:40:51.037][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-26 23:40:51.040][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-26 23:40:51.043][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:51.045][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:51.046][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:51.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:51.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:51.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:51.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:51.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:51.087][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:51.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:51.090][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.092][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.093][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.100][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:51.102][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:51.103][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.105][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:51.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:51.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.110][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:51.112][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:51.113][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:51.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:51.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.121][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:51.122][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:51.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.126][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:51.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:51.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.131][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:51.132][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:51.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.136][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:51.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:51.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.140][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:51.142][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:51.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.145][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:51.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:51.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.150][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:51.151][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.155][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:51.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.160][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:51.161][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:51.162][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.163][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:51.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:51.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.170][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:51.171][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:51.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.175][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:51.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:51.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.180][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:51.181][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:51.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.185][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:51.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:51.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.195][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:51.197][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:51.198][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.201][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:51.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:51.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:51.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:51.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.215][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:51.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:51.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:51.254][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-26 23:40:51.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:51.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:51.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:51.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:51.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:51.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:51.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:51.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:51.287][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[2025-03-26 23:40:51.288][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-26 23:40:51.290][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:51.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-26 23:40:51.293][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:51.295][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:51.296][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:51.297][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:51.298][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:51.299][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:51.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:51.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:51.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:51.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:51.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:51.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:51.328][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[2025-03-26 23:40:51.329][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-26 23:40:51.332][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:51.334][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:51.335][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-26 23:40:51.615][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-26 23:40:51.911][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:51.914][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-26 23:40:51.919][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-26 23:40:51.924][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-26 23:40:51.928][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:51.930][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:51.933][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:51.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:51.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:51.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:51.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:51.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:51.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:51.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:51.966][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.968][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.969][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.970][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:51.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:51.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.978][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:51.979][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:51.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.983][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:51.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:51.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.989][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:51.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:51.992][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:51.994][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:51.996][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:51.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:51.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.001][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:52.003][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:52.004][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:52.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:52.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.011][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:52.013][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:52.014][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.015][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:52.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:52.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.022][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:52.024][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:52.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.027][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.030][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:52.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:52.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.038][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:52.040][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.055][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:52.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.061][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:52.062][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:52.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:52.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:52.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.071][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:52.072][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:52.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:52.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:52.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.081][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:52.082][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:52.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.087][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:52.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:52.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.092][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:52.094][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:52.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.097][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:52.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:52.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:52.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:52.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:52.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:52.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:52.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:52.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:52.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:52.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:52.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:52.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:52.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:52.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:52.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:52.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:52.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:52.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:52.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.147][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:52.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:52.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:52.152][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-26 23:40:52.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:52.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:52.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:52.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:52.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:52.323][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:52.324][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:52.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:52.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:52.345][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:52.346][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[2025-03-26 23:40:52.347][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-26 23:40:52.349][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:52.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-26 23:40:52.353][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:52.355][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:52.357][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:52.359][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:52.361][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:52.363][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:52.367][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:52.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:52.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:52.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:52.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:52.387][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:52.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:52.390][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-26 23:40:52.393][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:52.394][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:52.396][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-26 23:40:52.678][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-26 23:40:52.973][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:52.976][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-26 23:40:52.980][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-26 23:40:52.984][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-26 23:40:52.986][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:52.988][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:52.989][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:52.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:52.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:52.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:53.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:53.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:53.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:53.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:53.006][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.008][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.009][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.016][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:53.018][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:53.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.021][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:53.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:53.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.026][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:53.028][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:53.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.030][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.031][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:53.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:53.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.036][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:53.037][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:53.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.040][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:53.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:53.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.046][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.047][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.050][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.057][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:53.058][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:53.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.063][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:53.064][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.065][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.067][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.068][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:53.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.074][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.075][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.077][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.085][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:53.086][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:53.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.091][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:53.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:53.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.096][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:53.098][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:53.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.100][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.102][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:53.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:53.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.107][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:53.109][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:53.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.113][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:53.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:53.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:53.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:53.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.124][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:53.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:53.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:53.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:53.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:53.174][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-26 23:40:53.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:53.192][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:53.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:53.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:53.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:53.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:53.212][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:53.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:53.215][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-26 23:40:53.216][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:53.218][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-26 23:40:53.221][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:53.222][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:53.224][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:53.226][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:53.227][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:53.228][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:53.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:53.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:53.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:53.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:53.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:53.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:53.261][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[2025-03-26 23:40:53.263][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-26 23:40:53.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:53.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:53.269][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-26 23:40:53.550][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-26 23:40:53.834][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:53.837][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-26 23:40:53.843][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-26 23:40:53.847][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-26 23:40:53.850][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:53.851][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:53.853][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:53.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:53.857][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:53.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:53.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:53.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:53.881][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:53.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:53.886][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.887][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.888][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:53.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:53.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.897][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:53.898][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:53.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.903][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:53.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:53.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.908][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:53.910][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:53.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.914][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:53.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:53.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.919][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:53.921][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:53.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.923][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.925][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:53.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:53.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.931][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.932][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.935][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:53.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.942][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:53.943][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:53.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.947][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:53.949][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.951][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.953][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:53.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:53.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.959][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.960][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.963][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:53.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.975][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:53.977][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:53.980][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.982][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:53.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:53.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:53.993][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:53.995][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:53.997][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:53.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.002][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:54.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:54.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.010][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:54.012][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:54.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.026][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.028][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:54.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:54.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:54.080][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-26 23:40:54.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:54.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:54.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:54.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:54.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:54.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:54.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:54.119][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.DEBUG[2025-03-26 23:40:54.121][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-26 23:40:54.122][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:54.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-26 23:40:54.126][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:54.127][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:54.128][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:54.130][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:54.131][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:54.132][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:54.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:54.136][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:54.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:54.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:54.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:54.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:54.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:54.165][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-26 23:40:54.171][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:54.172][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:54.173][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-26 23:40:54.454][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-26 23:40:54.735][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:54.738][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-26 23:40:54.742][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-26 23:40:54.746][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-26 23:40:54.749][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:54.750][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:54.752][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:54.754][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:54.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:54.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:54.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:54.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:54.765][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:54.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:54.769][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.770][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.772][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.779][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:54.780][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:54.781][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.784][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:54.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:54.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.789][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:54.790][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:54.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.794][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:54.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:54.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.799][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:54.800][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:54.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.802][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:54.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:54.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.809][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:54.810][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:54.811][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.812][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:54.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:54.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.819][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:54.820][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:54.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.822][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.824][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:54.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.827][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.829][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:54.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.834][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:54.835][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:54.836][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:54.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:54.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.844][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:54.845][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:54.847][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.850][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:54.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:54.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.855][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:54.856][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:54.857][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.858][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.860][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:54.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:54.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.865][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:54.866][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:54.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.870][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:54.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:54.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:54.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:54.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:54.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:54.926][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-26 23:40:54.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.932][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:54.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:54.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:54.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:54.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:54.943][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:54.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:54.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:54.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:54.969][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:54.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:54.971][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-26 23:40:54.972][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:54.974][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-26 23:40:54.976][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:54.977][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:54.978][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:54.980][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:54.981][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:54.982][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:54.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:54.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:54.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:55.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:55.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:55.002][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:55.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:55.005][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-26 23:40:55.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:55.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:55.011][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-26 23:40:55.292][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-26 23:40:55.573][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:55.576][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-26 23:40:55.581][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-26 23:40:55.585][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-26 23:40:55.587][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:55.589][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:55.590][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:55.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:55.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:55.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:55.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:55.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:55.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:55.616][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:55.619][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.620][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.622][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.623][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.630][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:55.631][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:55.632][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.634][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.636][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:55.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:55.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.642][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:55.643][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:55.645][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.646][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.647][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:55.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:55.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.659][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:55.664][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:55.665][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.666][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.668][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:55.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:55.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.674][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:55.675][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:55.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.677][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:55.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:55.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.684][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:55.685][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:55.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.687][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.689][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:55.690][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.692][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.694][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:55.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.699][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:55.700][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:55.701][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:55.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:55.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.709][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:55.710][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:55.711][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.713][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.715][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:55.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:55.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.720][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:55.722][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:55.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.725][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:55.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:55.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.730][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:55.731][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:55.733][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.734][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.735][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:55.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:55.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:55.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:55.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:55.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.752][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:55.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:55.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:55.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:55.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:55.798][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-26 23:40:55.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:55.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:55.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:55.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:55.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:55.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:55.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:55.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:55.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:55.829][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:55.830][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[2025-03-26 23:40:55.832][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-26 23:40:55.833][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:55.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-26 23:40:55.837][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:55.838][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:55.839][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:55.841][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:55.842][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:55.843][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:55.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:55.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:55.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:55.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:55.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:55.858][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:55.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:55.860][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-26 23:40:55.863][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:55.865][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:55.866][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-26 23:40:56.157][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-26 23:40:56.456][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:56.459][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-26 23:40:56.465][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-26 23:40:56.471][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-26 23:40:56.473][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:56.475][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:56.477][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:56.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:56.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:56.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:56.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:56.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:56.497][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:56.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:56.501][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.502][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.503][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.505][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.511][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:56.512][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:56.513][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.515][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.516][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:56.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:56.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.522][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:56.523][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:56.524][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.525][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:56.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:56.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.532][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:56.533][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:56.534][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.535][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:56.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:56.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:56.543][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:56.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.547][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:56.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:56.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.553][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.555][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:56.557][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:56.559][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.561][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.563][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:56.565][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.567][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:56.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.574][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:56.575][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:56.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.578][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:56.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:56.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.585][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:56.586][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:56.587][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:56.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:56.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.595][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:56.596][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:56.597][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.599][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:56.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:56.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.605][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:56.607][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:56.608][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.609][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:56.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:56.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:56.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:56.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:56.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:56.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:56.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:56.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.666][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:56.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:56.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:56.673][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-26 23:40:56.675][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:56.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:56.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:56.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:56.694][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:56.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:56.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:56.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:56.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:56.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:56.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:56.722][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-26 23:40:56.724][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:56.727][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-26 23:40:56.729][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:56.731][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:56.734][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:56.736][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:56.738][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:56.740][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:56.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:56.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:56.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:56.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:56.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:56.764][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:56.765][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.DEBUG[2025-03-26 23:40:56.767][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-26 23:40:56.780][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:56.782][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:56.783][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-26 23:40:57.063][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-26 23:40:57.348][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:57.352][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-26 23:40:57.359][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-26 23:40:57.365][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-26 23:40:57.368][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:57.370][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:57.373][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:57.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:57.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:57.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:57.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:57.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:57.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:57.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:57.406][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.408][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.411][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.417][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:57.419][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:57.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.421][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.423][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:57.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:57.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.427][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:57.429][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:57.430][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.431][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.433][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:57.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:57.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.439][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:57.440][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:57.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.444][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.446][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:57.448][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:57.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.452][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.454][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:57.456][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:57.457][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.458][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.460][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:57.461][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.465][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:57.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.471][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:57.473][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:57.474][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.475][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.477][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:57.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:57.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.482][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:57.484][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:57.486][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.487][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:57.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:57.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.495][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:57.496][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:57.497][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.498][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.500][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:57.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:57.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.505][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:57.506][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:57.507][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.508][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:57.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:57.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:57.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:57.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:57.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:57.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:57.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:57.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:57.562][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-26 23:40:57.564][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:57.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:57.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:57.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:57.586][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:57.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:57.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:57.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:57.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:57.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:57.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:57.611][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-26 23:40:57.612][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:57.614][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-26 23:40:57.616][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:57.617][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:57.619][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:57.620][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:57.621][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:57.622][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:57.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:57.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:57.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:57.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:57.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:57.637][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:57.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:57.640][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-26 23:40:57.643][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:57.644][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:57.646][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-26 23:40:57.933][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-26 23:40:58.213][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:40:58.216][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-26 23:40:58.220][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-26 23:40:58.224][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-26 23:40:58.227][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:40:58.228][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:40:58.230][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:40:58.232][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:58.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:58.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:59.305][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:59.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:59.308][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:59.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:40:59.312][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.313][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.314][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.315][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.322][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:59.323][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:59.324][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.325][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.327][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:40:59.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:40:59.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.331][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:59.333][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:59.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:40:59.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:40:59.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.342][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:40:59.343][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:40:59.344][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.345][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.347][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:40:59.348][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:40:59.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.350][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.352][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:59.353][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:40:59.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.356][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.357][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:59.358][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.359][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.362][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:40:59.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.367][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:59.368][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:59.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.371][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:59.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:40:59.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.377][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:59.379][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:59.380][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.381][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:40:59.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:40:59.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.388][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:59.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:59.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.391][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.394][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:40:59.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:40:59.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.401][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:40:59.403][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:40:59.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.406][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:59.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:59.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:59.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:59.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.426][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:40:59.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:40:59.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:40:59.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:40:59.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:59.460][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-26 23:40:59.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:40:59.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:40:59.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:40:59.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:40:59.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:59.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:59.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:59.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:59.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:59.505][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:59.506][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[2025-03-26 23:40:59.507][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-26 23:40:59.508][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:40:59.510][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-26 23:40:59.512][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:40:59.513][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:40:59.514][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:40:59.516][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:40:59.517][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:40:59.518][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:40:59.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:40:59.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:40:59.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:40:59.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:40:59.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:40:59.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:40:59.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:40:59.541][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-26 23:40:59.546][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:40:59.548][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:40:59.551][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-26 23:40:59.837][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-26 23:41:00.119][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:00.122][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-26 23:41:00.126][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-26 23:41:00.130][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-26 23:41:00.132][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:00.134][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:00.135][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:00.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:00.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:00.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:00.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:00.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:00.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:00.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:00.161][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.163][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.165][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.171][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:00.173][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:00.174][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.175][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.177][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:00.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:00.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.182][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:00.183][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:00.185][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.186][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.187][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:00.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:00.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.193][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:00.195][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:00.196][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.197][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.199][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:00.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:00.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.204][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:00.206][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:00.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.208][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:00.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:00.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.216][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:00.217][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:00.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.221][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:00.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.227][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:00.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.234][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:00.236][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:00.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:00.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:00.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.247][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:00.248][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:00.250][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:00.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:00.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.258][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:00.259][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:00.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.261][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.263][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:00.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:00.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.268][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:00.269][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:00.271][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.272][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.273][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:00.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:00.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:00.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:00.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:00.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:00.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:00.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:00.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:00.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:00.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:00.333][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-26 23:41:00.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:00.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:00.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:00.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:00.349][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:00.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:00.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:00.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:00.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:00.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:00.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:00.375][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-26 23:41:00.377][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:00.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-26 23:41:00.383][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:00.385][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:00.388][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:00.390][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:00.392][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:00.394][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:00.398][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:00.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:00.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:00.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:00.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:00.424][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:00.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:00.427][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-26 23:41:00.430][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:00.431][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:00.433][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-26 23:41:00.716][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-26 23:41:01.004][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:01.007][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-26 23:41:01.012][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-26 23:41:01.016][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-26 23:41:01.018][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:01.020][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:01.021][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:01.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:01.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:01.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:01.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:01.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:01.049][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:01.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:01.055][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.058][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.069][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:01.070][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:01.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:01.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:01.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.084][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:01.086][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:01.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.090][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:01.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:01.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.095][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:01.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:01.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.099][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:01.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:01.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.108][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:01.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:01.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.114][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.116][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:01.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:01.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.122][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:01.123][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:01.124][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.125][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.127][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:01.129][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.132][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.133][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:01.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.140][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:01.142][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:01.144][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.148][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:01.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:01.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.156][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:01.158][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:01.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.162][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.165][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:01.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:01.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:01.174][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:01.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.178][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.181][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:01.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:01.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.189][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:01.191][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:01.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.195][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.197][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:01.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:01.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:01.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:01.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:01.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:01.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:01.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:01.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:01.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:01.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:01.295][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-26 23:41:01.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:01.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:01.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:01.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:01.320][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:01.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:01.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:01.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:01.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:01.350][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:01.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:01.354][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-26 23:41:01.356][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:01.359][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-26 23:41:01.361][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:01.364][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:01.366][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:01.367][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:01.369][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:01.371][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:01.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:01.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:01.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:01.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:01.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:01.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:01.396][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:01.398][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-26 23:41:01.402][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:01.403][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:01.405][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-26 23:41:01.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-26 23:41:01.973][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:01.976][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-26 23:41:01.980][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-26 23:41:01.984][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-26 23:41:01.987][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:01.988][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:01.990][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:01.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:01.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:01.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:02.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:02.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:02.056][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:02.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:02.060][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.061][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.074][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:02.076][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:02.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.079][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.081][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:02.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:02.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.086][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:02.087][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:02.088][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.089][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:02.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:02.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.096][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:02.097][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:02.098][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.100][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.101][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:02.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:02.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.106][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.107][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.111][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.116][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:02.117][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:02.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.119][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.121][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:02.122][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.126][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:02.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.131][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:02.132][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:02.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.134][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:02.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:02.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.141][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:02.142][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:02.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.144][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.146][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:02.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:02.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.151][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:02.152][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:02.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.155][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:02.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:02.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.160][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:02.162][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:02.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.165][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:02.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:02.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:02.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:02.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:02.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:02.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:02.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:02.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:02.226][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-26 23:41:02.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:02.241][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:02.242][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:02.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:02.260][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:02.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:02.264][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:02.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:02.268][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-26 23:41:02.270][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:02.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-26 23:41:02.275][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:02.278][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:02.280][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:02.281][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:02.283][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:02.284][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:02.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:02.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:02.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:02.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:02.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:02.298][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:02.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:02.302][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-26 23:41:02.305][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:02.306][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:02.308][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-26 23:41:02.590][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-26 23:41:02.881][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:02.884][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-26 23:41:02.889][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-26 23:41:02.893][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-26 23:41:02.896][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:02.897][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:02.899][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:02.901][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:02.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:02.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:02.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:02.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:02.918][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:02.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:02.922][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.923][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.925][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:02.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:02.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.932][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:02.933][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:02.934][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.935][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.937][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:02.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:02.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.942][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:02.943][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:02.944][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.946][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:02.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:02.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.952][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:02.953][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:02.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.966][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:02.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:02.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.971][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.972][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.976][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:02.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.983][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:02.985][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:02.987][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.989][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:02.991][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:02.994][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:02.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:02.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.000][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:03.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:03.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.008][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:03.010][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:03.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:03.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:03.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.025][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:03.026][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:03.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.030][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:03.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:03.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.035][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:03.036][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:03.037][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.038][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:03.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:03.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.046][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:03.048][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:03.049][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.051][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.053][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:03.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:03.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:03.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:03.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:03.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:03.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:03.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:03.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:03.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:03.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:03.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:03.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:03.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:03.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:03.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:03.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:03.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:03.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:03.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:03.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:03.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:03.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:03.125][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-26 23:41:03.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:03.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:03.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:03.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:03.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:03.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:03.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:03.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:03.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:03.151][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:03.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:03.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:03.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:03.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:03.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:03.172][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[2025-03-26 23:41:03.173][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-26 23:41:03.175][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:03.177][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-26 23:41:03.178][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:03.180][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:03.181][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:03.182][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:03.183][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:03.185][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:03.187][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:03.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:03.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:03.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:03.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:03.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:03.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:03.214][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-26 23:41:03.217][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:03.218][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:03.220][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-26 23:41:03.498][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-26 23:41:03.986][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:03.989][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-26 23:41:03.993][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-26 23:41:03.997][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-26 23:41:04.000][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:04.001][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:04.003][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:04.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:04.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:04.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:04.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:04.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:04.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:04.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:04.029][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.030][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.031][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.032][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.039][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:04.040][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:04.041][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.042][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.044][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:04.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:04.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.049][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:04.050][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:04.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.052][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.054][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:04.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:04.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.059][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:04.060][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:04.061][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.063][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.064][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:04.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:04.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.070][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.072][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.073][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.079][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:04.080][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:04.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.084][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:04.086][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.089][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:04.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.094][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.095][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.104][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:04.105][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:04.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.109][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:04.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:04.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.114][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:04.115][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:04.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.119][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:04.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:04.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.124][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:04.125][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:04.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.129][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:04.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:04.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:04.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:04.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:04.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:04.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:04.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:04.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:04.205][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-26 23:41:04.207][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:04.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:04.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:04.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:04.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:04.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:04.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:04.253][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[2025-03-26 23:41:04.255][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-26 23:41:04.257][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:04.260][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-26 23:41:04.263][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:04.265][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:04.267][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:04.269][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:04.271][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:04.273][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:04.278][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:04.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:04.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:04.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:04.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:04.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:04.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:04.304][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-26 23:41:04.320][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:04.321][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:04.323][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-26 23:41:04.606][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-26 23:41:04.887][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:04.889][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-26 23:41:04.894][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-26 23:41:04.898][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-26 23:41:04.900][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:04.902][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:04.903][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:04.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:04.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:04.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:04.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:04.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:04.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:04.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:04.920][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.921][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.923][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:04.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.929][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:04.931][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:04.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.933][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.934][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:04.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:04.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.939][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:04.940][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:04.941][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.943][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.944][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:04.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:04.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.951][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:04.952][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:04.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.955][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.956][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:04.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:04.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.961][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.962][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.966][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:04.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.971][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:04.972][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:04.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.976][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:04.977][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.979][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.981][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:04.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:04.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.985][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.987][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.989][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:04.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:04.995][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:04.997][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:04.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:04.999][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.001][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:05.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:05.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.006][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:05.007][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:05.008][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.010][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.011][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:05.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:05.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.017][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:05.018][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:05.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.022][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:05.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:05.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:05.077][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-26 23:41:05.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:05.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:05.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:05.096][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:05.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:05.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:05.105][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:05.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:05.108][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-26 23:41:05.109][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:05.111][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-26 23:41:05.113][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:05.114][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:05.115][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:05.117][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:05.118][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:05.119][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:05.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:05.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:05.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:05.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:05.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:05.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:05.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:05.137][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-26 23:41:05.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:05.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:05.143][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-26 23:41:05.432][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-26 23:41:05.724][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:05.727][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-26 23:41:05.732][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-26 23:41:05.736][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-26 23:41:05.739][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:05.741][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:05.742][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:05.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:05.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:05.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:05.768][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:05.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:05.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:05.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:05.775][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.776][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.777][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.778][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.785][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:05.786][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:05.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.788][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.790][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:05.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:05.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.797][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:05.799][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:05.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.803][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.805][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:05.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:05.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.813][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:05.815][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:05.817][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.819][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.821][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:05.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:05.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.829][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:05.831][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:05.833][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.835][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.837][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:05.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:05.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.843][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:05.844][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:05.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.846][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.848][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:05.850][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.853][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.855][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:05.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:05.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:05.865][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:05.867][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:05.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:05.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.879][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:05.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:05.882][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.884][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.887][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:05.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:05.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.894][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:05.896][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:05.898][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.900][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.902][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:05.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:05.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.910][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:05.912][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:05.913][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.915][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.918][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:05.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:05.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:05.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:05.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:05.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:05.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:05.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:06.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:06.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:06.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.008][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-26 23:41:06.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.064][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[2025-03-26 23:41:06.068][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:06.070][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 23:41:06.072][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:06.075][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 23:41:06.080][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.082][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.110][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.TRACE[2025-03-26 23:41:06.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.120][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.202][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.337][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.475][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[2025-03-26 23:41:06.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.482][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.492][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.518][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.521][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.574][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.587][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.619][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.655][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.TRACE[2025-03-26 23:41:06.658][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.663][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.674][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.690][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.749][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[2025-03-26 23:41:06.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.784][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.TRACE[2025-03-26 23:41:06.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.851][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.852][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.865][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[2025-03-26 23:41:06.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.871][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.883][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.900][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.926][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.944][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.955][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:06.960][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:06.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:06.965][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:06.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:06.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:06.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:06.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:06.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:06.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:06.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:07.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:07.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:07.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:07.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:07.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:07.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:07.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:07.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:07.148][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[2025-03-26 23:41:07.152][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:07.154][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2025-03-26 23:41:07.156][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:07.188][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2025-03-26 23:41:07.192][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[2025-03-26 23:41:07.197][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:07.199][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2025-03-26 23:41:07.201][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:07.304][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2025-03-26 23:41:07.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:07.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:07.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:07.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:07.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:07.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:07.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:07.331][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-26 23:41:07.332][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:07.334][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-26 23:41:07.336][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:07.364][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml".
biodb.DEBUG[2025-03-26 23:41:07.365][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:07.367][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:07.369][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:07.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:07.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:07.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:07.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:07.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:07.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:07.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:07.396][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.398][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.402][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.410][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:07.411][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:07.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.413][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.415][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:07.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:07.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.420][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:07.422][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:07.423][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.424][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.426][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:07.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:07.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.432][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:07.435][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:07.437][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.439][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.441][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:07.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:07.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.450][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.453][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.455][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.456][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.467][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:07.469][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:07.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.473][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.475][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:07.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:07.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.484][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:07.486][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.490][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.492][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:07.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.502][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.527][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:07.529][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:07.531][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.533][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.535][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:07.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:07.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.544][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:07.546][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:07.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.552][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:07.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:07.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.560][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:07.563][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:07.564][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.566][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.569][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:07.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:07.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.577][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.601][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:07.654][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-26 23:41:07.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:07.679][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:07.680][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:07.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:07.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:07.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:07.701][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:07.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:07.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:07.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:07.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:07.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:07.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:07.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:07.742][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:07.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:07.746][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-26 23:41:07.748][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:07.752][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-26 23:41:07.755][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:07.782][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml".
biodb.DEBUG[2025-03-26 23:41:07.784][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:07.786][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:07.787][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:07.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:07.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:07.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:07.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:07.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:07.812][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:07.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:07.818][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.820][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.821][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.833][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:07.836][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:07.837][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.839][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.841][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:07.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:07.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.847][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:07.849][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:07.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.851][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.852][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:07.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:07.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.857][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:07.858][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:07.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:07.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:07.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.867][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.869][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.870][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.871][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.872][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:07.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.877][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:07.879][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:07.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.881][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.883][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:07.884][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.888][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:07.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:07.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.893][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.894][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.895][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.896][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:07.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.903][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:07.904][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:07.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.907][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.910][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:07.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:07.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.918][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:07.921][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:07.923][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.927][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:07.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:07.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.935][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:07.937][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:07.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.941][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.944][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:07.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:07.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:07.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:07.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:07.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:07.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:07.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:08.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:08.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:08.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:08.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:08.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:08.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:08.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:08.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:08.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:08.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:08.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:08.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:08.022][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:08.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:08.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:08.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:08.027][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-26 23:41:08.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:08.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:08.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:08.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:08.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:08.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:08.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:08.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:08.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:08.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:08.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:08.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:08.105][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2025-03-26 23:41:08.110][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2025-03-26 23:41:08.114][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:08.116][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:08.120][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:08.479][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:08.849][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:08.854][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-26 23:41:08.862][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-26 23:41:08.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:08.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:08.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.263][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.296][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.300][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.351][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.394][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.395][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.418][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.473][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.499][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.546][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.562][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.616][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.TRACE[2025-03-26 23:41:09.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.763][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.783][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.808][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.810][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[2025-03-26 23:41:09.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.819][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.821][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.907][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:09.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:09.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:09.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:09.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:09.957][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.TRACE[2025-03-26 23:41:09.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:09.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:09.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:09.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:09.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:09.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:09.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.149][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.171][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.172][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.TRACE[2025-03-26 23:41:10.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.200][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.227][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.288][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[2025-03-26 23:41:10.292][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:10.294][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-26 23:41:10.296][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:10.299][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-26 23:41:10.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.304][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.325][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.334][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.336][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.367][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.422][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.423][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.TRACE[2025-03-26 23:41:10.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.567][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.585][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.TRACE[2025-03-26 23:41:10.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.642][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.TRACE[2025-03-26 23:41:10.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.652][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.663][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.685][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.716][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.737][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.756][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.792][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.811][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.864][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.865][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[2025-03-26 23:41:10.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.887][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.909][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.923][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.958][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:10.974][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:10.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:10.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:10.983][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:10.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:10.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:10.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:10.988][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:10.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:10.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:11.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:11.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:11.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:11.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:11.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:11.030][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:11.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:11.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:11.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:11.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:11.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:11.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:11.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:11.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:11.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:11.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:11.086][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:11.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:11.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:11.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:11.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:11.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:11.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:11.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:11.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:11.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:11.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:11.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:11.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:11.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:11.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:11.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:11.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:11.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:11.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:11.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:11.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:11.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:11.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:11.221][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:11.242][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:11.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:11.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:11.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:11.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:11.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:11.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:11.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:11.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.311][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:11.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:11.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 23:41:11.339][biodb::testThat]
biodb.INFO [2025-03-26 23:41:11.341][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-26 23:41:11.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:11.343][biodb::testThat]
biodb.TRACE[2025-03-26 23:41:11.347][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 23:41:11.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 23:41:11.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:11.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:11.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:11.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:11.382][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:11.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:11.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:11.396][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:11.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:11.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:11.400][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:11.406][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[2025-03-26 23:41:11.412][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:11.415][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:11.419][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:11.702][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:11.988][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:11.990][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-26 23:41:11.995][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-26 23:41:12.000][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:12.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:12.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:12.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:12.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:12.017][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:12.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:12.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:12.042][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 23:41:12.047][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:12.049][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:12.053][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:12.356][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:12.665][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2025-03-26 23:41:12.668][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-03-26 23:41:12.674][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-26 23:41:12.681][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-26 23:41:12.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:12.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:12.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:12.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:12.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:12.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:12.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:12.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:12.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:12.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:12.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:12.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:12.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:12.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:12.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:12.781][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:12.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:12.798][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 23:41:12.800][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:12.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:12.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:12.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:12.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:12.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:12.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:12.825][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.835][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.837][private$selectFields]
biodb.TRACE[2025-03-26 23:41:12.838][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:12.840][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:12.842][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.846][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.848][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.850][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.852][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.857][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.858][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.859][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.860][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.862][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.863][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.864][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:12.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.895][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-26 23:41:12.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:12.898][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:12.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:12.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:12.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:12.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:12.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:12.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.929][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.930][private$selectFields]
biodb.TRACE[2025-03-26 23:41:12.932][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:12.933][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:12.934][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.936][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.937][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.938][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.939][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.941][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.947][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.948][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:12.950][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.952][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.954][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.956][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.957][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:12.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:12.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:12.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:12.982][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 23:41:12.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:12.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:12.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:12.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:13.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:13.001][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:13.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:13.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.018][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:13.020][private$selectFields]
biodb.TRACE[2025-03-26 23:41:13.022][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:13.024][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:13.026][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:13.028][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.030][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.033][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.035][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.038][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.041][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.043][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:13.045][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:13.047][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.049][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.051][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.053][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.054][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:13.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.072][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-26 23:41:13.073][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 23:41:13.074][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 23:41:13.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:13.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:13.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:13.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:13.215][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:13.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:13.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:13.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:13.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:13.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:13.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:13.303][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 23:41:13.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:13.311][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:13.313][private$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[2025-03-26 23:41:13.604][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[2025-03-26 23:41:13.887][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:13.891][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-26 23:41:13.898][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-26 23:41:13.905][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[2025-03-26 23:41:13.911][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:13.913][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:13.916][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:14.206][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:14.500][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:14.503][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-26 23:41:14.511][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-26 23:41:14.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:14.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:14.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:14.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:14.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:14.555][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:14.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:14.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:14.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:14.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:14.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:14.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:14.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:14.600][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:14.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:14.628][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:14.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:14.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:14.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:14.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:14.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:14.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:14.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.665][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:14.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:14.690][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 23:41:14.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:14.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:14.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:14.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:14.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:14.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:14.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:14.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.749][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.751][private$selectFields]
biodb.TRACE[2025-03-26 23:41:14.752][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:14.753][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:14.754][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.755][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.760][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.761][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.763][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.764][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.765][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.766][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.767][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.769][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.772][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:14.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.788][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-26 23:41:14.789][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:14.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:14.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:14.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:14.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:14.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:14.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:14.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.847][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.848][private$selectFields]
biodb.TRACE[2025-03-26 23:41:14.849][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:14.850][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:14.851][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.853][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.854][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.856][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.857][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.859][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.860][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.862][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.871][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.873][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.874][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.875][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.878][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:14.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.893][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 23:41:14.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:14.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:14.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:14.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:14.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:14.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:14.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:14.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.933][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.935][private$selectFields]
biodb.TRACE[2025-03-26 23:41:14.937][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:14.938][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:14.940][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.941][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.942][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.946][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.947][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.949][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.950][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.952][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.954][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:14.956][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.958][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.960][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.962][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.964][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:14.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:14.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:14.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:14.989][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-26 23:41:14.991][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 23:41:14.993][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 23:41:15.026][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:15.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:15.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 23:41:15.054][biodb::testThat]
biodb.INFO [2025-03-26 23:41:15.055][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-26 23:41:15.057][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:15.058][biodb::testThat]
biodb.TRACE[2025-03-26 23:41:15.064][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 23:41:15.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 23:41:15.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:15.098][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:15.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:15.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:15.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:15.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:15.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:15.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:15.122][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-26 23:41:15.127][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:15.129][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:15.132][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:15.422][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:15.707][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:15.711][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-26 23:41:15.718][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-26 23:41:15.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:15.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:15.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:15.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:15.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:15.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:15.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:15.745][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.755][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:15.761][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[2025-03-26 23:41:15.765][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:15.766][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-26 23:41:15.768][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:15.771][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-26 23:41:15.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:15.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:15.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:15.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:15.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:15.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:15.787][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.TRACE[2025-03-26 23:41:15.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:15.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:15.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:15.806][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:15.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:15.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:15.823][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:15.825][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[2025-03-26 23:41:15.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:15.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:15.844][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 23:41:15.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:15.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:15.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:15.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:15.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:15.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:15.870][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.TRACE[2025-03-26 23:41:15.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.880][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.885][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:15.886][private$selectFields]
biodb.TRACE[2025-03-26 23:41:15.888][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:15.889][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:15.890][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:15.891][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.893][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.894][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.897][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.899][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.902][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.904][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:15.905][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:15.907][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.909][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.911][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.914][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:15.916][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.938][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-26 23:41:15.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:15.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:15.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:15.953][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:15.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:15.957][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:15.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:15.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.975][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:15.977][private$selectFields]
biodb.TRACE[2025-03-26 23:41:15.979][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:15.981][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:15.983][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:15.985][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.987][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.990][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.992][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.994][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:15.995][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:15.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:15.998][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:15.999][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.000][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.002][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.004][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.006][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:16.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.027][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 23:41:16.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:16.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.195][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.197][private$selectFields]
biodb.TRACE[2025-03-26 23:41:16.199][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:16.201][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:16.203][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.207][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.209][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.211][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.213][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.215][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.221][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.223][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.225][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.229][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.233][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:16.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.259][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-26 23:41:16.260][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 23:41:16.262][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 23:41:16.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:16.311][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.328][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[2025-03-26 23:41:16.333][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[2025-03-26 23:41:16.338][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:16.341][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-26 23:41:16.344][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:16.347][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-26 23:41:16.363][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[2025-03-26 23:41:16.367][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:16.369][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-26 23:41:16.371][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:16.374][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-26 23:41:16.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.593][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.597][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.TRACE[2025-03-26 23:41:16.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:16.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.640][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:16.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:16.667][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.668][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.670][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:16.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:16.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:16.715][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 23:41:16.718][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:16.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.761][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.763][private$selectFields]
biodb.TRACE[2025-03-26 23:41:16.765][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:16.766][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:16.768][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.770][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.776][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.778][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.780][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.784][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.785][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.787][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.789][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.791][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.793][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.795][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.797][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:16.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.817][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-26 23:41:16.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:16.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.865][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.867][private$selectFields]
biodb.TRACE[2025-03-26 23:41:16.869][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:16.871][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:16.873][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.875][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.877][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.879][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.881][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.883][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.885][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.886][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.890][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.892][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.894][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.896][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.899][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.901][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:16.903][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.926][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 23:41:16.928][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:16.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:16.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:16.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:16.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:16.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:16.950][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.TRACE[2025-03-26 23:41:16.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.962][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.964][private$selectFields]
biodb.TRACE[2025-03-26 23:41:16.966][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:16.967][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:16.969][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.972][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.974][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.980][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.982][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.984][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.986][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:16.988][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.990][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:16.991][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.994][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:16.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:16.998][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.000][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:17.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.010][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.020][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-26 23:41:17.021][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 23:41:17.022][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 23:41:17.034][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:17.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:17.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 23:41:17.045][biodb::testThat]
biodb.INFO [2025-03-26 23:41:17.048][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-26 23:41:17.050][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:17.052][biodb::testThat]
biodb.TRACE[2025-03-26 23:41:17.058][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-26 23:41:17.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-26 23:41:17.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.067][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.075][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.136][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[2025-03-26 23:41:17.141][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[2025-03-26 23:41:17.146][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:17.149][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-26 23:41:17.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:17.154][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-26 23:41:17.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.169][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.193][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[2025-03-26 23:41:17.196][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:17.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-26 23:41:17.200][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:17.202][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-26 23:41:17.205][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.234][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.240][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.252][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:17.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.274][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 23:41:17.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.321][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.322][private$selectFields]
biodb.TRACE[2025-03-26 23:41:17.324][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:17.325][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:17.326][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.328][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.329][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.331][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.332][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.333][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.335][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.336][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.338][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.339][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.341][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.342][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.343][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.344][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:17.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.355][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.363][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-26 23:41:17.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.389][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.408][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.410][private$selectFields]
biodb.TRACE[2025-03-26 23:41:17.411][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:17.413][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:17.415][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.416][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.418][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.420][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.422][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.423][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.424][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.425][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.427][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.428][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.429][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.430][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.432][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.433][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.434][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.435][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:17.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.454][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 23:41:17.456][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.457][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.505][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.508][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.509][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.TRACE[2025-03-26 23:41:17.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.520][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.521][private$selectFields]
biodb.TRACE[2025-03-26 23:41:17.522][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:17.524][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:17.525][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.526][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.527][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.529][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.531][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.535][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.537][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.538][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.540][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.542][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.544][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.546][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.548][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.550][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.552][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:17.554][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.578][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-26 23:41:17.579][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 23:41:17.581][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 23:41:17.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.669][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.671][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.688][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[2025-03-26 23:41:17.697][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[2025-03-26 23:41:17.703][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:17.706][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-26 23:41:17.709][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:17.713][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-26 23:41:17.719][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[2025-03-26 23:41:17.723][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:17.725][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-26 23:41:17.727][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:17.730][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-26 23:41:17.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.747][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.752][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[2025-03-26 23:41:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.778][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.794][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.796][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.861][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:17.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:17.869][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-26 23:41:17.872][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.886][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.899][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.900][private$selectFields]
biodb.TRACE[2025-03-26 23:41:17.901][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:17.902][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:17.903][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.904][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.906][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.907][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.908][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.915][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.917][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.918][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.919][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.920][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.921][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.922][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.924][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.926][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.927][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:17.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.933][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.943][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-26 23:41:17.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:17.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:17.946][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:17.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:17.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:17.956][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:17.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:17.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.968][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.969][private$selectFields]
biodb.TRACE[2025-03-26 23:41:17.971][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:17.972][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:17.973][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.974][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.975][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.978][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.979][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.981][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.983][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.984][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.986][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.988][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:17.990][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.992][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:17.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:17.996][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:17.998][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:18.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.020][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-26 23:41:18.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:18.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:18.024][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:18.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:18.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:18.040][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:18.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:18.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.055][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:18.056][private$selectFields]
biodb.TRACE[2025-03-26 23:41:18.057][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-26 23:41:18.058][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-26 23:41:18.060][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:18.061][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.062][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.065][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.066][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.067][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.070][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:18.072][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-26 23:41:18.073][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.075][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.077][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.078][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-26 23:41:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.089][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:18.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:18.094][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-26 23:41:18.095][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-26 23:41:18.097][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-26 23:41:18.131][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-26 23:41:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:18.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-26 23:41:18.142][biodb::testThat]
biodb.INFO [2025-03-26 23:41:18.143][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-26 23:41:18.145][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:18.146][biodb::testThat]
biodb.DEBUG[2025-03-26 23:41:18.148][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-26 23:41:18.149][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:18.151][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-26 23:41:18.153][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:18.154][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:18.156][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:18.157][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:18.158][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:18.159][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:18.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:18.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:18.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:18.174][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:18.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:18.177][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:18.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:18.179][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-26 23:41:18.183][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:18.184][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:18.186][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-26 23:41:18.476][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-26 23:41:18.860][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:18.863][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-26 23:41:18.867][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-26 23:41:18.871][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-26 23:41:18.874][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:18.875][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:18.877][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:18.879][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:18.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:18.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:19.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:19.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:19.062][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:19.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:19.066][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.067][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.068][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.069][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.076][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:19.077][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:19.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.080][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.081][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:19.083][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:19.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.087][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:19.088][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:19.089][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.090][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.092][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:19.093][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:19.095][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.096][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.097][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:19.099][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:19.100][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.101][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.103][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:19.104][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:19.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.108][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:19.109][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:19.110][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.111][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.113][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:19.114][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:19.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.118][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:19.119][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:19.121][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.123][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:19.125][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:19.126][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.127][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:19.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:19.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:19.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:19.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:19.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:19.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:19.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:19.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:19.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:19.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:19.200][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-26 23:41:19.202][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-26 23:41:19.229][biodb::testThat]
biodb.INFO [2025-03-26 23:41:19.230][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-26 23:41:19.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:19.233][biodb::testThat]
biodb.DEBUG[2025-03-26 23:41:19.252][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-26 23:41:19.254][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-26 23:41:19.255][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-26 23:41:19.257][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-26 23:41:19.259][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-26 23:41:19.261][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:19.262][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:19.263][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:19.265][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:19.266][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:19.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:19.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:19.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:19.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:19.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:19.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:19.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:19.305][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-26 23:41:19.308][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:19.310][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:19.311][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-26 23:41:19.597][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-26 23:41:19.882][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:19.886][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-26 23:41:19.890][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-26 23:41:19.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:19.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:19.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:19.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:19.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:19.915][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:19.916][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[2025-03-26 23:41:19.917][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-26 23:41:19.921][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:19.922][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:19.924][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-26 23:41:20.210][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-26 23:41:20.498][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:20.501][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-26 23:41:20.506][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-26 23:41:20.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:20.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:20.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:20.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:20.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:20.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:20.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:20.522][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-26 23:41:20.526][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:20.528][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:20.530][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-26 23:41:20.820][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-26 23:41:21.290][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:21.294][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-26 23:41:21.299][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-26 23:41:21.306][private$doSaveContentToFile] Saving to cache [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-26 23:41:21.697][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:21.699][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-26 23:41:21.701][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:21.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:21.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:21.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:21.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:21.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:21.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:21.719][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[2025-03-26 23:41:21.723][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.724][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.726][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.727][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.735][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:21.737][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:21.738][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.742][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:21.743][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:21.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.748][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:21.750][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:21.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.753][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.755][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:21.756][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:21.758][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.759][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.761][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:21.763][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:21.764][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.766][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.768][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:21.770][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:21.771][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.773][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.774][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:21.776][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:21.778][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.779][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.781][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:21.782][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:21.784][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.785][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.787][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:21.789][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:21.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.794][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:21.795][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:21.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.798][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:21.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:21.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:21.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:21.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:21.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:21.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:21.846][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:21.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:21.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:21.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:21.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:21.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:21.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:21.871][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.873][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.874][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.876][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:21.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:21.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.884][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:21.885][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:21.887][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.888][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.890][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:21.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:21.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.896][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:21.898][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:21.899][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:21.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:21.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.909][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:21.911][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:21.912][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.914][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:21.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:21.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.922][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:21.923][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:21.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.926][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:21.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:21.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.934][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:21.936][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:21.937][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.939][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.941][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:21.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:21.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.947][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:21.949][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:21.950][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.951][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.953][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:21.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:21.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.960][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:21.961][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:21.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:21.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:21.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.972][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:21.974][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:21.975][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:21.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:21.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.985][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:21.987][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:21.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.990][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.991][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:21.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:21.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:21.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:21.998][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:21.999][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:22.001][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.002][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.004][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:22.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:22.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:22.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:22.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:22.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:22.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:22.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:22.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:22.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:22.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:22.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:22.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:22.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:22.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:22.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:22.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:22.055][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:22.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:22.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:22.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:22.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:22.579][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:22.581][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.TRACE[2025-03-26 23:41:22.586][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:22.588][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:22.590][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.591][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:22.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:22.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.906][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:22.908][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:22.909][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.911][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.913][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:22.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:22.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:22.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:22.920][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:22.922][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:22.924][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.160][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:23.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:23.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.167][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:23.169][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:23.170][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:23.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:23.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.180][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:23.464][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:23.466][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.467][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.469][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:23.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:23.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.476][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:23.491][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:23.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.494][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.496][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:23.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:23.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.847][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:23.849][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:23.851][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.854][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:23.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:23.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.860][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:23.862][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:23.863][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.865][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:23.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:23.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.873][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:23.874][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:23.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.877][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:23.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:23.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.886][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:23.887][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:23.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.892][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:23.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:23.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.898][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:23.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:23.901][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.903][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:23.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:23.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:23.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:23.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:23.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:23.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:23.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:23.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:23.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:23.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:23.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:24.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:24.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:24.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:24.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:24.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:24.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:24.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:24.011][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-26 23:41:24.012][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-26 23:41:24.014][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-26 23:41:24.156][biodb::testThat]
biodb.INFO [2025-03-26 23:41:24.158][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-26 23:41:24.159][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:24.161][biodb::testThat]
biodb.INFO [2025-03-26 23:41:24.721][biodb::testThat]
biodb.INFO [2025-03-26 23:41:24.724][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-26 23:41:24.726][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:24.728][biodb::testThat]
biodb.INFO [2025-03-26 23:41:24.810][biodb::testThat]
biodb.INFO [2025-03-26 23:41:24.812][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-26 23:41:24.814][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:24.815][biodb::testThat]
biodb.DEBUG[2025-03-26 23:41:24.821][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[2025-03-26 23:41:24.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:24.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:24.831][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:25.171][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:25.546][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:25.551][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-26 23:41:25.559][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-26 23:41:25.601][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:25.603][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:25.605][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:25.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:25.607][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:25.609][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:25.610][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:25.611][ef$get] fields variable is a list.
biodb.INFO [2025-03-26 23:41:25.614][biodb::testThat]
biodb.INFO [2025-03-26 23:41:25.615][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-26 23:41:25.616][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:25.617][biodb::testThat]
biodb.ERROR[2025-03-26 23:41:25.648][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-26 23:41:25.666][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-26 23:41:25.689][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 23:41:25.691][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 23:41:25.692][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 23:41:25.694][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 23:41:25.695][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:25.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:25.697][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:25.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:25.699][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 23:41:25.713][biodb::testContext]
biodb.INFO [2025-03-26 23:41:25.714][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:41:25.716][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-26 23:41:25.717][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:41:25.718][biodb::testContext]
biodb.INFO [2025-03-26 23:41:25.721][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:41:25.723][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 23:41:25.729][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:25.730][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 23:41:25.731][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 23:41:25.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.736][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 23:41:25.737][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 23:41:25.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.742][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 23:41:25.743][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 23:41:25.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.747][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.DEBUG[2025-03-26 23:41:25.748][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 23:41:25.749][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 23:41:25.750][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 23:41:25.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.755][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 23:41:25.756][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 23:41:25.758][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 23:41:25.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.762][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 23:41:25.764][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 23:41:25.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.770][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 23:41:25.771][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 23:41:25.773][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 23:41:25.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.780][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 23:41:25.782][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 23:41:25.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.789][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 23:41:25.792][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 23:41:25.794][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 23:41:25.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.801][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:41:25.802][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 23:41:25.804][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 23:41:25.805][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 23:41:25.806][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 23:41:25.808][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 23:41:25.809][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.814][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 23:41:25.816][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 23:41:25.817][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.830][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 23:41:25.831][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 23:41:25.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.836][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 23:41:25.838][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 23:41:25.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.841][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[2025-03-26 23:41:25.842][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 23:41:25.844][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 23:41:25.845][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.848][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 23:41:25.849][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 23:41:25.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.854][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:41:25.855][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 23:41:25.858][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 23:41:25.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.864][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 23:41:25.866][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 23:41:25.868][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 23:41:25.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:25.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:25.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:25.875][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 23:41:25.877][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.878][self$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[2025-03-26 23:41:25.880][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.882][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:25.883][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.884][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.885][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.886][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.888][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:41:25.889][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:25.890][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.891][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 23:41:25.893][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:25.894][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.895][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.896][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:25.896][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:25.896][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:25.896][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:41:25.896][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:41:25.898][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:25.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:25.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:25.901][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:25.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:25.904][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:25.905][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.906][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.907][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:25.908][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:25.910][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.911][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.912][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 23:41:25.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.916][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:41:25.917][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.918][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:25.920][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.921][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.922][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.924][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.925][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:41:25.926][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:25.927][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.929][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 23:41:25.930][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:25.931][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.932][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.934][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:25.934][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:25.934][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:25.934][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:41:25.934][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:41:25.935][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:25.936][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:25.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:25.938][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:25.940][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:25.941][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:25.942][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.943][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.944][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:25.945][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:25.947][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.948][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.949][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 23:41:25.951][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.953][self$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[2025-03-26 23:41:25.954][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.955][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:25.956][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.959][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.960][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.962][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:41:25.963][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:25.965][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.966][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 23:41:25.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:25.969][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.971][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.973][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.975][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:25.977][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:25.978][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:25.980][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:25.981][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:25.982][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:25.983][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:25.985][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.986][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:25.987][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:25.988][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:25.989][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:25.991][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 23:41:25.993][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.994][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:41:25.995][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.997][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:25.998][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:25.999][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:26.000][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:26.001][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:26.003][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:41:26.004][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:26.005][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:26.006][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 23:41:26.008][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:26.009][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:26.010][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:26.011][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:26.012][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:26.014][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:26.015][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:26.016][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:26.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:26.018][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:26.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:26.021][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:26.022][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:26.023][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:26.024][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:26.025][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:26.027][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:26.028][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.036][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.040][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.DEBUG[2025-03-26 23:41:26.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.046][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[2025-03-26 23:41:26.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.051][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[2025-03-26 23:41:26.052][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.074][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[2025-03-26 23:41:26.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.125][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 23:41:26.127][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 23:41:26.128][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 23:41:26.130][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 23:41:26.132][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:41:26.133][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 23:41:26.135][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 23:41:26.136][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 23:41:26.138][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 23:41:26.140][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 23:41:26.141][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:41:26.143][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 23:41:26.144][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 23:41:26.146][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 23:41:26.148][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 23:41:26.149][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 23:41:26.151][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 23:41:26.152][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 23:41:26.154][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:41:26.156][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 23:41:26.157][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 23:41:26.159][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 23:41:26.161][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 23:41:26.162][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 23:41:26.164][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 23:41:26.166][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 23:41:26.168][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 23:41:26.170][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 23:41:26.171][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 23:41:26.173][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 23:41:26.174][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 23:41:26.176][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 23:41:26.177][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 23:41:26.179][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 23:41:26.181][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 23:41:26.182][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 23:41:26.184][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 23:41:26.185][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 23:41:26.187][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 23:41:26.188][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 23:41:26.190][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 23:41:26.191][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 23:41:26.193][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 23:41:26.195][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 23:41:26.196][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 23:41:26.198][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 23:41:26.200][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 23:41:26.201][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 23:41:26.203][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 23:41:26.204][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 23:41:26.206][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 23:41:26.207][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 23:41:26.209][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 23:41:26.211][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 23:41:26.212][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 23:41:26.214][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 23:41:26.215][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 23:41:26.217][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 23:41:26.218][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 23:41:26.220][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 23:41:26.222][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 23:41:26.223][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 23:41:26.225][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 23:41:26.226][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 23:41:26.228][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 23:41:26.229][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 23:41:26.231][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:41:26.233][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:41:26.234][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 23:41:26.236][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 23:41:26.237][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 23:41:26.239][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 23:41:26.240][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 23:41:26.242][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 23:41:26.250][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 23:41:26.252][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 23:41:26.253][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 23:41:26.255][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 23:41:26.257][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 23:41:26.258][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 23:41:26.260][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 23:41:26.262][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 23:41:26.263][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 23:41:26.265][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 23:41:26.267][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:41:26.268][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:26.269][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.272][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.295][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[2025-03-26 23:41:26.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.310][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[2025-03-26 23:41:26.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.325][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[2025-03-26 23:41:26.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.342][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.391][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.393][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:26.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:26.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:26.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:26.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:26.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:26.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:26.408][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 23:41:26.410][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 23:41:26.412][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:26.413][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 23:41:26.415][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:26.416][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:26.417][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:26.418][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:26.420][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:26.421][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 23:41:26.422][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 23:41:26.423][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:26.425][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:26.426][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 23:41:26.427][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 23:41:26.428][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 23:41:26.430][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:26.431][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:26.431][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:26.431][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:26.432][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 23:41:26.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:26.435][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:26.436][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:26.437][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:26.438][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:26.439][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:26.440][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:26.440][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 23:41:26.442][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:26.443][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:26.444][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:26.446][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 23:41:26.446][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 23:41:26.448][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:41:26.450][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:41:26.451][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 23:41:26.453][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:41:26.455][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:41:26.456][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:41:26.460][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 23:41:26.461][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 23:41:26.462][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 23:41:26.464][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 23:41:26.466][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:41:26.467][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:41:26.469][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 23:41:26.470][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 23:41:26.472][biodb::testThat]
biodb.INFO [2025-03-26 23:41:26.473][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-03-26 23:41:26.474][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:26.475][biodb::testThat]
biodb.DEBUG[2025-03-26 23:41:26.479][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 23:41:26.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:26.486][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:26.487][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-26 23:41:26.769][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-26 23:41:27.144][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:27.147][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-26 23:41:27.153][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-26 23:41:27.159][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[2025-03-26 23:41:27.163][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:27.164][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:27.166][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:27.450][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:27.737][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:27.741][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-26 23:41:27.746][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-26 23:41:27.749][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:27.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:27.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:27.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:27.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:27.901][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:27.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:27.904][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 23:41:27.909][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:27.910][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:27.912][private$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[2025-03-26 23:41:28.202][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[2025-03-26 23:41:28.493][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:28.496][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-26 23:41:28.501][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-26 23:41:28.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:28.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:28.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:28.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:28.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:28.535][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:28.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:28.564][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:28.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:28.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:28.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:28.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:28.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:28.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:28.594][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[2025-03-26 23:41:28.600][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:28.603][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-26 23:41:28.606][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:28.610][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-26 23:41:28.614][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:28.616][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:28.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:28.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:28.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:28.638][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:28.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:28.644][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[2025-03-26 23:41:28.650][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:28.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-26 23:41:28.655][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:28.659][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-26 23:41:28.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:28.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:28.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:28.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:28.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:28.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:28.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:28.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:28.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:28.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:28.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:28.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:28.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:28.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:28.751][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[2025-03-26 23:41:28.755][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:28.757][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-26 23:41:28.759][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:28.762][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-26 23:41:28.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:28.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:28.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:28.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:28.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:28.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:28.787][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[2025-03-26 23:41:28.790][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[2025-03-26 23:41:28.794][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:28.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-26 23:41:28.797][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:28.800][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-26 23:41:28.802][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:28.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:28.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:28.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:28.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:28.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:28.824][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[2025-03-26 23:41:28.827][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[2025-03-26 23:41:28.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:28.832][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:28.834][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:29.115][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:29.399][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:29.404][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-26 23:41:29.412][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-26 23:41:29.417][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:29.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:29.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:29.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:29.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:29.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:29.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 23:41:29.460][biodb::testThat]
biodb.INFO [2025-03-26 23:41:29.462][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-03-26 23:41:29.463][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:29.464][biodb::testThat]
biodb.DEBUG[2025-03-26 23:41:29.468][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 23:41:29.472][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:29.474][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:29.476][private$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[2025-03-26 23:41:29.759][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[2025-03-26 23:41:30.043][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:30.047][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-26 23:41:30.053][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-26 23:41:30.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:30.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:30.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:30.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:30.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:30.070][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.071][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[2025-03-26 23:41:30.076][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[2025-03-26 23:41:30.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:30.081][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:30.083][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-26 23:41:30.369][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-26 23:41:30.656][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:30.660][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-26 23:41:30.667][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-26 23:41:30.672][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:30.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:30.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:30.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:30.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:30.693][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 23:41:30.702][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 23:41:30.704][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 23:41:30.705][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 23:41:30.706][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 23:41:30.707][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:30.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:30.709][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:30.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:30.711][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-26 23:41:30.721][biodb::testContext]
biodb.INFO [2025-03-26 23:41:30.723][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:41:30.725][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-26 23:41:30.727][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:41:30.728][biodb::testContext]
biodb.INFO [2025-03-26 23:41:30.733][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:41:30.736][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 23:41:30.745][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:30.747][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 23:41:30.749][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 23:41:30.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.753][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 23:41:30.754][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 23:41:30.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.759][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 23:41:30.760][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 23:41:30.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.764][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 23:41:30.766][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 23:41:30.767][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 23:41:30.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.771][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 23:41:30.772][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 23:41:30.774][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 23:41:30.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.777][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[2025-03-26 23:41:30.778][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 23:41:30.779][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 23:41:30.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.786][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 23:41:30.788][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 23:41:30.790][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 23:41:30.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.793][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.797][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 23:41:30.799][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 23:41:30.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.806][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 23:41:30.808][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 23:41:30.810][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 23:41:30.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.817][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:41:30.819][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 23:41:30.820][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 23:41:30.822][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 23:41:30.824][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 23:41:30.826][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 23:41:30.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.832][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 23:41:30.834][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 23:41:30.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.839][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[2025-03-26 23:41:30.840][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 23:41:30.842][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 23:41:30.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.849][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 23:41:30.850][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 23:41:30.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.854][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[2025-03-26 23:41:30.855][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 23:41:30.856][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 23:41:30.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.861][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 23:41:30.862][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 23:41:30.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.865][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.DEBUG[2025-03-26 23:41:30.866][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:41:30.868][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 23:41:30.871][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 23:41:30.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.875][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 23:41:30.877][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 23:41:30.878][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 23:41:30.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:30.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:30.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:30.883][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 23:41:30.884][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.886][self$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[2025-03-26 23:41:30.887][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:30.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.891][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.895][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.897][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:41:30.899][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:30.901][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.903][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 23:41:30.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:30.907][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.908][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.910][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:30.910][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:30.910][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:30.910][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:41:30.910][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:41:30.911][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:30.912][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:30.913][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:30.914][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:30.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:30.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:30.918][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.919][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.920][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:30.921][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:30.922][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.924][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.925][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 23:41:30.927][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.928][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:41:30.929][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.930][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:30.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.936][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:41:30.938][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:30.939][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.940][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 23:41:30.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:30.942][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.944][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.945][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:30.945][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:30.945][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:30.945][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:41:30.945][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:41:30.946][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:30.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:30.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:30.950][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:30.951][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:30.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:30.953][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.954][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.956][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:30.957][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:30.958][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.959][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.960][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 23:41:30.962][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.964][self$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[2025-03-26 23:41:30.965][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.966][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:30.967][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.968][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.969][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.971][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.972][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:41:30.973][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:30.974][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:30.976][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 23:41:30.977][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:30.978][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.979][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:30.980][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.982][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:30.983][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:30.984][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:30.985][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:30.986][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:30.987][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:30.988][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:30.990][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:30.991][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:30.998][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:31.006][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:31.008][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:31.010][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 23:41:31.012][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.014][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:41:31.015][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.017][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:31.019][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:31.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:31.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:31.024][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:41:31.026][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:31.027][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:31.028][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 23:41:31.030][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:31.031][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:31.032][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.034][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:31.035][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:31.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:31.039][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:31.040][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:31.041][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:31.042][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:31.043][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:31.044][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:31.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:31.047][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:31.048][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:31.049][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:31.051][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:31.053][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.071][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[2025-03-26 23:41:31.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.088][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[2025-03-26 23:41:31.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.104][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[2025-03-26 23:41:31.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.110][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[2025-03-26 23:41:31.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.151][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.167][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.171][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 23:41:31.173][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 23:41:31.175][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 23:41:31.177][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 23:41:31.178][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:41:31.180][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 23:41:31.181][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 23:41:31.184][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 23:41:31.186][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 23:41:31.187][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 23:41:31.189][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:41:31.190][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 23:41:31.192][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 23:41:31.194][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 23:41:31.196][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 23:41:31.197][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 23:41:31.199][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 23:41:31.200][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 23:41:31.202][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:41:31.203][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 23:41:31.205][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 23:41:31.206][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 23:41:31.208][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 23:41:31.210][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 23:41:31.212][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 23:41:31.213][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 23:41:31.215][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 23:41:31.217][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 23:41:31.219][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 23:41:31.220][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 23:41:31.222][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 23:41:31.224][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 23:41:31.226][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 23:41:31.228][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 23:41:31.230][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 23:41:31.232][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 23:41:31.235][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 23:41:31.237][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 23:41:31.240][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 23:41:31.242][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 23:41:31.245][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 23:41:31.247][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 23:41:31.249][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 23:41:31.250][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 23:41:31.252][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 23:41:31.254][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 23:41:31.256][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 23:41:31.258][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 23:41:31.261][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 23:41:31.263][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 23:41:31.265][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 23:41:31.268][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 23:41:31.270][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 23:41:31.273][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 23:41:31.275][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 23:41:31.277][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 23:41:31.280][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 23:41:31.282][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 23:41:31.285][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 23:41:31.287][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 23:41:31.290][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 23:41:31.292][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 23:41:31.295][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 23:41:31.297][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 23:41:31.300][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 23:41:31.302][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 23:41:31.305][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:41:31.308][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:41:31.310][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 23:41:31.313][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 23:41:31.315][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 23:41:31.318][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 23:41:31.321][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 23:41:31.323][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 23:41:31.326][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 23:41:31.328][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 23:41:31.331][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 23:41:31.333][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 23:41:31.336][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 23:41:31.339][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 23:41:31.341][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 23:41:31.344][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 23:41:31.347][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 23:41:31.349][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 23:41:31.353][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:41:31.355][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:31.357][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.360][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.432][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.455][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.DEBUG[2025-03-26 23:41:31.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.463][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.473][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[2025-03-26 23:41:31.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.482][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.DEBUG[2025-03-26 23:41:31.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.520][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[2025-03-26 23:41:31.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:31.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:31.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:31.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:31.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:31.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:31.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:31.542][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 23:41:31.545][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 23:41:31.549][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:31.550][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 23:41:31.551][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.553][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:31.554][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:31.556][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.557][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 23:41:31.558][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 23:41:31.560][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:31.561][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.562][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 23:41:31.563][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 23:41:31.564][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 23:41:31.566][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:31.568][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:31.568][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:31.568][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:31.569][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 23:41:31.571][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:31.572][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:31.573][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:31.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:31.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:31.577][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:31.578][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:31.578][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 23:41:31.580][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:31.581][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:31.583][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:31.584][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 23:41:31.584][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 23:41:31.587][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:41:31.590][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:41:31.593][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 23:41:31.595][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:41:31.598][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:41:31.601][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:41:31.606][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 23:41:31.608][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 23:41:31.609][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 23:41:31.612][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 23:41:31.613][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:41:31.614][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:41:31.616][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 23:41:31.617][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 23:41:31.619][biodb::testThat]
biodb.INFO [2025-03-26 23:41:31.620][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-26 23:41:31.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:31.623][biodb::testThat]
biodb.DEBUG[2025-03-26 23:41:31.626][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 23:41:31.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:31.633][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-26 23:41:31.634][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:31.638][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-26 23:41:31.642][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-26 23:41:31.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:31.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:31.650][private$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[2025-03-26 23:41:31.937][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[2025-03-26 23:41:32.234][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:32.237][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-26 23:41:32.242][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-26 23:41:32.254][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 23:41:32.256][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 23:41:32.257][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 23:41:32.258][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 23:41:32.260][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.262][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.264][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.265][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.INFO [2025-03-26 23:41:32.271][biodb::testContext]
biodb.INFO [2025-03-26 23:41:32.272][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:41:32.273][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-26 23:41:32.274][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-26 23:41:32.275][biodb::testContext]
biodb.INFO [2025-03-26 23:41:32.278][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:41:32.281][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-26 23:41:32.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:32.288][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-26 23:41:32.290][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-26 23:41:32.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.297][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-26 23:41:32.299][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-26 23:41:32.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.305][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[2025-03-26 23:41:32.306][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-26 23:41:32.309][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-26 23:41:32.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.316][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-26 23:41:32.317][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-26 23:41:32.320][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-26 23:41:32.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.324][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.DEBUG[2025-03-26 23:41:32.325][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-26 23:41:32.326][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-26 23:41:32.327][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-26 23:41:32.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.332][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-26 23:41:32.333][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-26 23:41:32.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.336][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[2025-03-26 23:41:32.338][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-26 23:41:32.339][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-26 23:41:32.340][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-26 23:41:32.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.345][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-26 23:41:32.346][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-26 23:41:32.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.349][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[2025-03-26 23:41:32.350][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-26 23:41:32.352][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-26 23:41:32.353][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-26 23:41:32.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.356][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.357][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:41:32.359][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-26 23:41:32.360][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-26 23:41:32.361][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-26 23:41:32.362][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-26 23:41:32.363][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-26 23:41:32.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.368][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-26 23:41:32.369][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-26 23:41:32.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.374][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-26 23:41:32.375][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-26 23:41:32.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.381][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-26 23:41:32.382][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-26 23:41:32.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.387][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-26 23:41:32.388][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-26 23:41:32.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.392][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-26 23:41:32.394][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-26 23:41:32.395][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.398][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-26 23:41:32.399][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-26 23:41:32.403][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-26 23:41:32.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.406][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[2025-03-26 23:41:32.407][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-26 23:41:32.409][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-26 23:41:32.410][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-26 23:41:32.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.416][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-26 23:41:32.418][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.420][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-26 23:41:32.421][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.423][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:32.425][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.428][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.430][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.431][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:41:32.432][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:32.434][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.435][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-26 23:41:32.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:32.437][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.440][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:32.440][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:32.440][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:32.440][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:41:32.440][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:41:32.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:32.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.444][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.446][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:32.448][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.452][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.454][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.456][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:32.457][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:32.459][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.461][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.464][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-26 23:41:32.467][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.469][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:41:32.471][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.473][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:32.475][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.476][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.478][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.480][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.482][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:41:32.484][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:32.486][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.488][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-26 23:41:32.490][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:32.492][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.494][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.496][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:32.496][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:32.496][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:32.496][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-26 23:41:32.496][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-26 23:41:32.498][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:32.500][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.502][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.503][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:32.505][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.507][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.509][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.511][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.513][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:32.514][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:32.516][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.518][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.520][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-26 23:41:32.522][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.523][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-26 23:41:32.524][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.525][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:32.526][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.528][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.529][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.531][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.532][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-26 23:41:32.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:32.534][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.536][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-26 23:41:32.537][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:32.538][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.539][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.540][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.542][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:32.543][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.545][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.547][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:32.549][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.550][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.552][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.554][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.556][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:32.558][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:32.560][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.561][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.563][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-26 23:41:32.566][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.568][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-26 23:41:32.570][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.572][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:32.574][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.575][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.577][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.579][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.581][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-26 23:41:32.583][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:32.585][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.587][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-26 23:41:32.589][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:32.591][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.593][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:32.595][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.597][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-26 23:41:32.599][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.601][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.603][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:32.604][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:32.605][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:32.607][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:32.608][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.609][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:32.619][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:32.620][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:32.621][self$setPropertyValue]
biodb.DEBUG[2025-03-26 23:41:32.623][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:32.625][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.628][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.634][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.639][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[2025-03-26 23:41:32.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.646][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.653][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[2025-03-26 23:41:32.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.665][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[2025-03-26 23:41:32.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.673][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[2025-03-26 23:41:32.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.690][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[2025-03-26 23:41:32.692][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.708][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.718][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.725][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[2025-03-26 23:41:32.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.759][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.DEBUG[2025-03-26 23:41:32.761][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-26 23:41:32.764][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-26 23:41:32.767][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-26 23:41:32.769][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-26 23:41:32.772][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:41:32.774][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-26 23:41:32.777][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-26 23:41:32.779][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-26 23:41:32.782][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-26 23:41:32.784][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-26 23:41:32.787][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:41:32.789][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-26 23:41:32.792][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-26 23:41:32.795][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-26 23:41:32.797][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-26 23:41:32.800][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-26 23:41:32.803][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-26 23:41:32.805][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-26 23:41:32.808][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:41:32.811][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-26 23:41:32.813][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-26 23:41:32.816][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-26 23:41:32.818][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-26 23:41:32.821][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-26 23:41:32.824][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-26 23:41:32.826][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-26 23:41:32.829][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-26 23:41:32.831][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-26 23:41:32.834][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-26 23:41:32.837][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-26 23:41:32.839][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-26 23:41:32.842][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-26 23:41:32.845][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-26 23:41:32.847][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-26 23:41:32.850][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-26 23:41:32.851][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-26 23:41:32.853][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-26 23:41:32.855][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-26 23:41:32.856][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-26 23:41:32.858][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-26 23:41:32.859][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-26 23:41:32.861][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-26 23:41:32.863][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-26 23:41:32.865][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-26 23:41:32.866][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-26 23:41:32.868][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-26 23:41:32.869][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-26 23:41:32.871][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-26 23:41:32.872][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-26 23:41:32.874][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-26 23:41:32.875][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-26 23:41:32.877][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-26 23:41:32.879][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-26 23:41:32.880][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-26 23:41:32.882][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-26 23:41:32.884][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-26 23:41:32.885][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-26 23:41:32.887][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-26 23:41:32.889][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-26 23:41:32.891][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-26 23:41:32.893][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-26 23:41:32.896][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-26 23:41:32.898][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-26 23:41:32.900][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-26 23:41:32.902][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-26 23:41:32.903][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-26 23:41:32.905][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:41:32.906][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:41:32.908][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-26 23:41:32.909][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-26 23:41:32.911][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-26 23:41:32.912][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-26 23:41:32.914][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-26 23:41:32.916][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-26 23:41:32.917][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-26 23:41:32.919][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-26 23:41:32.920][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-26 23:41:32.922][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-26 23:41:32.923][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-26 23:41:32.925][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-26 23:41:32.926][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-26 23:41:32.928][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-26 23:41:32.929][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-26 23:41:32.931][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-26 23:41:32.933][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-26 23:41:32.935][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-26 23:41:32.936][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.938][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.940][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.DEBUG[2025-03-26 23:41:32.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.967][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[2025-03-26 23:41:32.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.976][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:32.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:32.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:32.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:32.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:32.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:32.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:32.998][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.DEBUG[2025-03-26 23:41:33.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.046][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[2025-03-26 23:41:33.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.055][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.061][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[2025-03-26 23:41:33.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-26 23:41:33.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.080][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-26 23:41:33.082][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-26 23:41:33.084][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:33.086][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-26 23:41:33.087][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:33.088][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-26 23:41:33.089][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:33.091][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-26 23:41:33.092][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:33.093][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-26 23:41:33.101][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-26 23:41:33.102][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-26 23:41:33.104][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:33.105][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-26 23:41:33.106][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-26 23:41:33.107][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-26 23:41:33.109][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-26 23:41:33.110][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-26 23:41:33.110][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-26 23:41:33.110][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-26 23:41:33.112][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-26 23:41:33.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:33.114][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:33.115][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-26 23:41:33.116][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-26 23:41:33.117][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-26 23:41:33.119][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-26 23:41:33.121][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:33.121][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-26 23:41:33.123][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-26 23:41:33.125][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-26 23:41:33.127][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-26 23:41:33.128][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-26 23:41:33.128][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-26 23:41:33.130][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-26 23:41:33.132][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-26 23:41:33.134][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-26 23:41:33.137][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-26 23:41:33.140][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-26 23:41:33.142][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-26 23:41:33.148][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-26 23:41:33.149][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-26 23:41:33.152][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-26 23:41:33.155][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-26 23:41:33.157][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:41:33.158][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-26 23:41:33.161][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-26 23:41:33.162][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-26 23:41:33.165][biodb::testThat]
biodb.INFO [2025-03-26 23:41:33.167][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-26 23:41:33.169][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-26 23:41:33.171][biodb::testThat]
biodb.DEBUG[2025-03-26 23:41:33.176][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-26 23:41:33.183][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:33.186][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-26 23:41:33.189][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:33.193][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-26 23:41:33.199][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[2025-03-26 23:41:33.205][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-26 23:41:33.207][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-26 23:41:33.210][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-26 23:41:33.214][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-26 23:41:33.240][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-26 23:41:33.242][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-26 23:41:33.245][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-26 23:41:33.248][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-26 23:41:33.250][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-26 23:41:33.252][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-26 23:41:33.254][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-26 23:41:33.256][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-26 23:41:33.258][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-26 23:41:33.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:33.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:33.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:33.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:33.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:33.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:33.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-26 23:41:33.285][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-26 23:41:33.290][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-26 23:41:33.292][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-26 23:41:33.294][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-26 23:41:33.586][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-26 23:41:34.148][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-26 23:41:34.152][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-26 23:41:34.159][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-26 23:41:34.163][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-26 23:41:34.167][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-26 23:41:34.170][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-26 23:41:34.172][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-26 23:41:34.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-26 23:41:34.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:34.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:34.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:34.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:34.205][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:34.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-26 23:41:34.215][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.218][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.220][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.221][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.224][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.232][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:34.234][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:34.236][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.238][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.240][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-26 23:41:34.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-26 23:41:34.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.248][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:34.250][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:34.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.257][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-26 23:41:34.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-26 23:41:34.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.265][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-26 23:41:34.267][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-26 23:41:34.268][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.270][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.273][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-26 23:41:34.275][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-26 23:41:34.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.281][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:34.284][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:34.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.290][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:34.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-26 23:41:34.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.298][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:34.300][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:34.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.304][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.306][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-26 23:41:34.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-26 23:41:34.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.314][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:34.316][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:34.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.320][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:34.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-26 23:41:34.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.330][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:34.331][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:34.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.334][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.336][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-26 23:41:34.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-26 23:41:34.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.341][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:34.342][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:34.343][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.344][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.346][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-26 23:41:34.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-26 23:41:34.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.351][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:34.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:34.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.356][ef$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.359][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-26 23:41:34.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-26 23:41:34.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:34.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:34.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:34.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:34.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-26 23:41:34.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-26 23:41:34.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.421][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-26 23:41:34.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-26 23:41:34.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-26 23:41:34.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-26 23:41:34.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-26 23:41:34.436][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-26 23:41:34.451][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-26 23:41:34.452][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-26 23:41:34.454][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-26 23:41:34.455][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-26 23:41:34.456][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-26 23:41:34.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-26 23:41:34.458][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-26 23:41:34.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-26 23:41:34.460][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-26 23:41:34.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 384 ]
> 
> proc.time()
   user  system elapsed 
  25.79    2.12   57.40

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	4.18	2.25	152.14
ChebiEntry	0.51	0.01	0.53