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"	4777
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4458
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: 2025-03-19 23:12:28 -0400 (Wed, 19 Mar 2025)

EndedAt: 2025-03-19 23:22:05 -0400 (Wed, 19 Mar 2025)

EllapsedTime: 577.0 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 4.34   2.52  207.06
* 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 [2025-03-19 23:19:37.432][biodb::testContext]
biodb.INFO [2025-03-19 23:19:37.435][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:19:37.437][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-03-19 23:19:37.438][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:19:37.440][biodb::testContext]
biodb.INFO [2025-03-19 23:19:37.447][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:19:37.450][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 23:19:37.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:19:37.461][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 23:19:37.463][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 23:19:37.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.468][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 23:19:37.499][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 23:19:37.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.503][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 23:19:37.505][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 23:19:37.506][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.508][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.509][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 23:19:37.510][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 23:19:37.512][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 23:19:37.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.516][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 23:19:37.517][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 23:19:37.519][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 23:19:37.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.523][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 23:19:37.524][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 23:19:37.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.528][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[2025-03-19 23:19:37.529][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 23:19:37.530][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 23:19:37.531][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 23:19:37.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.536][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 23:19:37.537][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 23:19:37.538][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.541][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 23:19:37.543][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 23:19:37.544][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 23:19:37.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.548][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:19:37.550][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 23:19:37.551][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 23:19:37.552][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 23:19:37.553][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 23:19:37.554][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 23:19:37.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.559][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 23:19:37.560][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 23:19:37.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.565][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 23:19:37.566][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 23:19:37.567][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.570][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 23:19:37.572][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 23:19:37.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.576][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 23:19:37.577][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 23:19:37.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.581][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[2025-03-19 23:19:37.583][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 23:19:37.585][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 23:19:37.587][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.591][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:19:37.593][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 23:19:37.598][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 23:19:37.599][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.603][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 23:19:37.604][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 23:19:37.605][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 23:19:37.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.612][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 23:19:37.639][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.653][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-19 23:19:37.655][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.656][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:19:37.657][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.660][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.661][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.662][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:19:37.663][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:19:37.664][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.666][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 23:19:37.667][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:19:37.668][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.669][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.671][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:19:37.671][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:19:37.671][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:19:37.671][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:19:37.671][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:19:37.677][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:19:37.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.681][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:19:37.682][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.683][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.684][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.685][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.686][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:19:37.687][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:19:37.689][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.690][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.691][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 23:19:37.693][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.694][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:19:37.695][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.697][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:19:37.698][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.699][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.700][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.701][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.702][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:19:37.704][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:19:37.705][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.706][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 23:19:37.707][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:19:37.709][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.710][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.711][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:19:37.711][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:19:37.711][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:19:37.711][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:19:37.711][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:19:37.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:19:37.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.716][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:19:37.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.719][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.720][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:19:37.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:19:37.724][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.725][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.726][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 23:19:37.728][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.729][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-19 23:19:37.731][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.732][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:19:37.733][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.734][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.735][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.737][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.738][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:19:37.739][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:19:37.740][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.742][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 23:19:37.743][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:19:37.744][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.745][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.746][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.747][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:19:37.749][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.750][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.751][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:19:37.752][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.753][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.754][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.756][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.757][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:19:37.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:19:37.759][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.760][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.762][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 23:19:37.763][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.765][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:19:37.766][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.767][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:19:37.768][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.771][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.772][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.773][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:19:37.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:19:37.776][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.777][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 23:19:37.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:19:37.779][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.780][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:37.781][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.783][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:19:37.784][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.785][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.786][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:19:37.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:37.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:37.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:19:37.791][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.792][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:19:37.793][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:19:37.794][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:37.796][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:19:37.799][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:19:37.800][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.809][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.812][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[2025-03-19 23:19:37.813][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.819][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.835][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.839][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[2025-03-19 23:19:37.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.895][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:37.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:37.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:37.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:37.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:37.901][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 23:19:37.905][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 23:19:37.907][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 23:19:37.909][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 23:19:37.910][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:19:37.912][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 23:19:37.913][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 23:19:37.915][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 23:19:37.916][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 23:19:37.918][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 23:19:37.920][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:19:37.921][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 23:19:37.923][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 23:19:37.924][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 23:19:37.926][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 23:19:37.927][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 23:19:37.929][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 23:19:37.930][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 23:19:37.932][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:19:37.934][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 23:19:37.935][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 23:19:37.937][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 23:19:37.939][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 23:19:37.942][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 23:19:37.944][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 23:19:37.945][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 23:19:37.947][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 23:19:37.948][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 23:19:37.950][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 23:19:37.952][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 23:19:37.953][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 23:19:37.955][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 23:19:37.956][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 23:19:37.958][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 23:19:37.959][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 23:19:37.961][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 23:19:37.963][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 23:19:37.964][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 23:19:37.966][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 23:19:37.967][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 23:19:37.969][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 23:19:37.970][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 23:19:37.972][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 23:19:37.973][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 23:19:37.975][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 23:19:37.977][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 23:19:37.978][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 23:19:37.980][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 23:19:37.981][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 23:19:37.983][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 23:19:37.984][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 23:19:37.986][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 23:19:37.988][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 23:19:37.991][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 23:19:37.993][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 23:19:37.996][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 23:19:37.998][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 23:19:38.001][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 23:19:38.003][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 23:19:38.006][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 23:19:38.008][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 23:19:38.010][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 23:19:38.011][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 23:19:38.013][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 23:19:38.014][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 23:19:38.016][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 23:19:38.018][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:19:38.019][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:19:38.021][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 23:19:38.022][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 23:19:38.024][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 23:19:38.025][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 23:19:38.027][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 23:19:38.028][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 23:19:38.030][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 23:19:38.031][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 23:19:38.033][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 23:19:38.034][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 23:19:38.036][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 23:19:38.038][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 23:19:38.039][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 23:19:38.041][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 23:19:38.042][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 23:19:38.067][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 23:19:38.070][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:19:38.073][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:19:38.074][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.076][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.082][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.096][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[2025-03-19 23:19:38.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.104][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[2025-03-19 23:19:38.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.121][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.132][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.133][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[2025-03-19 23:19:38.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.140][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[2025-03-19 23:19:38.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.148][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.159][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.DEBUG[2025-03-19 23:19:38.161][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.184][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.186][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:19:38.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:19:38.247][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 23:19:38.263][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 23:19:38.267][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:38.270][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 23:19:38.272][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:38.274][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:19:38.276][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:38.278][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:19:38.279][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:38.281][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 23:19:38.283][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 23:19:38.285][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:19:38.287][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:38.289][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 23:19:38.291][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 23:19:38.293][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 23:19:38.295][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 23:19:38.297][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:19:38.297][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:19:38.297][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:19:38.299][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 23:19:38.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:38.302][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:38.304][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:19:38.306][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:19:38.308][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:19:38.309][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:19:38.311][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:19:38.311][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 23:19:38.313][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:19:38.315][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:19:38.317][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 23:19:38.319][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 23:19:38.319][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 23:19:38.328][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:19:38.331][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:19:38.334][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 23:19:38.337][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:19:38.340][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:19:38.343][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:19:38.375][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 23:19:38.378][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 23:19:38.381][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 23:19:38.385][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 23:19:38.389][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:19:38.390][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:19:38.392][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 23:19:38.393][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 23:19:38.455][biodb::testThat]
biodb.INFO [2025-03-19 23:19:38.457][biodb::testThat] Running test function  test.entry.fields  (" Entry fields have a correct value ").
biodb.INFO [2025-03-19 23:19:38.459][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:19:38.461][biodb::testThat]
biodb.TRACE[2025-03-19 23:19:38.518][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-03-19 23:19:38.520][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:19:38.524][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:19:38.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:19:38.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:38.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:38.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:38.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:38.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:38.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:19:38.580][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.581][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.601][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:38.603][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:38.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.605][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.628][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:38.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:38.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.634][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:38.635][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:38.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.637][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:38.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:38.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.643][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:38.645][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:38.646][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.647][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:38.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:38.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.654][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.655][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.656][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.657][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.664][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:38.665][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:38.666][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.667][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.669][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:38.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:38.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.674][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:19:38.675][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:38.676][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.678][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.679][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:19:38.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:38.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.684][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:38.686][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:38.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.688][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:38.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:38.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.695][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:38.696][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:38.697][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.707][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:38.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:38.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.716][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:19:38.718][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:38.720][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.722][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.724][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:19:38.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:38.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.732][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:38.734][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:38.736][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.738][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.740][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:38.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:38.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:38.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:38.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.755][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:38.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:38.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:38.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:38.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:19:38.859][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-03-19 23:19:38.862][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:38.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:38.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:38.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:38.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.896][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:38.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:38.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:38.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:38.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:38.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.916][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 23:19:38.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 23:19:38.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.921][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 23:19:38.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 23:19:38.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.926][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-19 23:19:38.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-19 23:19:38.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.932][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-19 23:19:38.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-19 23:19:38.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:38.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:38.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:38.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:38.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.070][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.112][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.114][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.116][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.162][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.167][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.168][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.171][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.172][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:39.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.188][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:39.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:39.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:39.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:39.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.199][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:39.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:39.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.204][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:39.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:39.206][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.207][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.208][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:39.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:39.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:39.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:39.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.241][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:39.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:39.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:39.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:39.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.255][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:39.257][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:39.259][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.260][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.262][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:39.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:39.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.288][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.303][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.304][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.305][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.306][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.384][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.409][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.411][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.413][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.465][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:39.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:39.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.470][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:39.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:39.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.475][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:39.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:39.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.480][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:39.481][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:39.482][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.484][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.485][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:39.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:39.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.499][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.504][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.510][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.515][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.516][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.517][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.518][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.520][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.534][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.540][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.544][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.549][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.550][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.553][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.554][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.569][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:39.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:39.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.574][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:39.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:39.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.582][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:39.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:39.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.589][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:39.591][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:39.592][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.593][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.594][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:39.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:39.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.623][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.638][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.639][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.641][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.642][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.643][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.671][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:39.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:39.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.676][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:39.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:39.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:39.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:39.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.686][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:39.687][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:39.688][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.690][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.691][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:39.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:39.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.713][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:39.715][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:39.716][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.727][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:39.729][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:39.730][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.732][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.753][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:39.755][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:39.757][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.758][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.780][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:39.781][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:39.783][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.784][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.791][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.793][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:39.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.809][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.810][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:39.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.823][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:39.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.829][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.840][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.841][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:39.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.844][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.862][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.864][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:39.865][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.866][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.880][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:39.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:39.885][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.887][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:39.899][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:39.900][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:39.902][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:39.903][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 23:19:39.923][biodb::testThat]
biodb.INFO [2025-03-19 23:19:39.924][biodb::testThat] Running test function  test.rt.unit  (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-03-19 23:19:39.926][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:19:39.927][biodb::testThat]
biodb.DEBUG[2025-03-19 23:19:39.946][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-03-19 23:19:39.956][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:19:39.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-03-19 23:19:39.968][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:19:39.972][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-03-19 23:19:39.974][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:19:40.011][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:19:40.014][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:19:40.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:19:40.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:19:40.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:19:40.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:19:40.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:19:40.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:19:40.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:19:40.043][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.045][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.047][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.049][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.086][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:40.089][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:40.091][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.095][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:19:40.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:19:40.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.104][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:40.106][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:40.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:19:40.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:19:40.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.120][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:40.122][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:40.123][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.124][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.125][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:19:40.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:19:40.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.131][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:40.132][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:40.133][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.135][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:19:40.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:19:40.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.143][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:40.144][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:40.145][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.146][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.148][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:40.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:19:40.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.153][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:19:40.154][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:40.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:19:40.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:19:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.170][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:40.171][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:40.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.175][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:40.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:19:40.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.180][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:40.181][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:40.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.184][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:40.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:40.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.190][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:19:40.192][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:40.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.196][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:19:40.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:19:40.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.204][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:40.206][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:40.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.212][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:19:40.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:19:40.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:40.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:40.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:40.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:40.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:19:40.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:19:40.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:19:40.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:19:40.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:19:40.269][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-03-19 23:19:40.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-03-19 23:19:40.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-03-19 23:19:40.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.275][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-03-19 23:19:40.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-03-19 23:19:40.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-03-19 23:19:40.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-03-19 23:19:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 23:19:40.317][biodb::testThat]
biodb.INFO [2025-03-19 23:19:40.319][biodb::testThat] Running test function  test.searchForEntries  (" We can search for an entry by searchable field ").
biodb.INFO [2025-03-19 23:19:40.320][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:19:40.321][biodb::testThat]
biodb.TRACE[2025-03-19 23:19:40.325][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:40.327][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:40.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.330][ef$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:19:40.332][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-03-19 23:19:40.372][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:40.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:40.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.377][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:40.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:40.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:19:40.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:19:40.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:19:40.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:19:40.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:19:40.390][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-03-19 23:19:40.395][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 23:19:40.413][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:19:40.415][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:19:40.417][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-03-19 23:20:28.400][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-03-19 23:20:28.786][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:28.790][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-03-19 23:20:28.810][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-03-19 23:20:28.834][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:20:28.849][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:28.850][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:28.876][private$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[2025-03-19 23:20:29.427][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[2025-03-19 23:20:29.964][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:29.969][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-03-19 23:20:29.977][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-03-19 23:20:29.981][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2025-03-19 23:20:30.011][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:30.013][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:30.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.018][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.020][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.022][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.024][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.025][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 23:20:30.034][biodb::testThat]
biodb.INFO [2025-03-19 23:20:30.036][biodb::testThat] Running test function  test.searchByName  (" We can search for an entry by name. ").
biodb.INFO [2025-03-19 23:20:30.037][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:20:30.038][biodb::testThat]
biodb.TRACE[2025-03-19 23:20:30.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:30.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:30.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:30.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:30.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:30.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:30.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:30.198][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[2025-03-19 23:20:30.204][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:20:30.229][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 23:20:30.232][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:20:30.274][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-03-19 23:20:30.337][biodb::testThat]
biodb.INFO [2025-03-19 23:20:30.339][biodb::testThat] Running test function  testEntryLoading  (" We can load an entry from the database. ").
biodb.INFO [2025-03-19 23:20:30.340][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:20:30.350][biodb::testThat]
biodb.TRACE[2025-03-19 23:20:30.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:30.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:30.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:30.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:30.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.429][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.436][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.443][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-19 23:20:30.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-19 23:20:30.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.450][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-19 23:20:30.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-19 23:20:30.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:30.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:30.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:30.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:30.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:30.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:30.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.538][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.546][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-03-19 23:20:30.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.555][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-03-19 23:20:30.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-03-19 23:20:30.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:30.563][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-03-19 23:20:30.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-03-19 23:20:30.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:30.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 23:20:30.586][biodb::testThat]
biodb.INFO [2025-03-19 23:20:30.588][biodb::testThat] Running test function  test.entry.page.url  (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-03-19 23:20:30.590][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:20:30.593][biodb::testThat]
biodb.INFO [2025-03-19 23:20:30.613][biodb::testThat]
biodb.INFO [2025-03-19 23:20:30.615][biodb::testThat] Running test function  test.entry.image.url  (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-03-19 23:20:30.617][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:20:30.619][biodb::testThat]
biodb.INFO [2025-03-19 23:20:30.639][biodb::testThat]
biodb.INFO [2025-03-19 23:20:30.641][biodb::testThat] Running test function  test.entry.page.url.download  (" The entry page URL can be downloaded. ").
biodb.INFO [2025-03-19 23:20:30.643][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:20:30.645][biodb::testThat]
biodb.DEBUG[2025-03-19 23:20:30.653][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-03-19 23:20:31.206][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-03-19 23:20:32.331][biodb::testThat]
biodb.INFO [2025-03-19 23:20:32.333][biodb::testThat] Running test function  test.entry.image.url.download  (" The entry image URL can be downloaded. ").
biodb.INFO [2025-03-19 23:20:32.335][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:20:32.336][biodb::testThat]
biodb.DEBUG[2025-03-19 23:20:32.702][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[2025-03-19 23:20:33.066][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:33.068][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:33.069][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.072][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:33.073][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:33.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.076][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 23:20:33.078][biodb::testThat]
biodb.INFO [2025-03-19 23:20:33.079][biodb::testThat] Running test function  test.searchCompound  (" We can search for a compound ").
biodb.INFO [2025-03-19 23:20:33.081][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:20:33.082][biodb::testThat]
biodb.TRACE[2025-03-19 23:20:33.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:33.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:33.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.127][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:33.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:33.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:33.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:33.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:33.270][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[2025-03-19 23:20:33.276][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:20:33.291][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 23:20:33.294][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:20:33.298][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 23:20:33.394][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[2025-03-19 23:20:33.400][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:20:33.401][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 23:20:33.404][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:20:33.408][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-03-19 23:20:33.444][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 23:20:33.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 23:20:33.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:33.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:33.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:33.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:33.501][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[2025-03-19 23:20:33.505][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:33.506][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:33.508][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:20:33.823][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:20:34.147][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:34.151][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-03-19 23:20:34.158][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-03-19 23:20:34.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:34.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:34.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:34.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:34.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:34.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:34.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:34.371][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2025-03-19 23:20:34.425][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:34.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2025-03-19 23:20:34.429][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:34.431][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:34.432][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:34.433][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:34.435][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:34.436][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:34.439][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:34.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:34.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:34.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:34.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:34.616][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:34.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:34.621][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2025-03-19 23:20:34.626][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:34.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:34.631][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2025-03-19 23:20:34.968][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2025-03-19 23:20:35.283][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:35.287][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2025-03-19 23:20:35.294][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2025-03-19 23:20:35.300][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2025-03-19 23:20:35.305][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:35.308][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:35.310][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:35.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:35.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:35.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:35.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:35.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:35.330][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:35.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:35.337][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.338][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.347][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.356][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:35.358][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:35.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.361][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.364][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:35.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:35.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.372][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:35.374][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:35.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.377][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.380][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:35.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:35.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.389][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:35.391][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:35.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.395][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.397][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:35.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.405][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:35.407][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:35.409][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.411][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.413][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:35.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.421][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:35.423][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:35.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.426][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.429][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:35.431][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.432][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.434][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.436][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:35.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.444][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:35.446][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:35.448][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.449][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:35.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.457][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:35.458][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:35.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.461][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.462][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:35.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:35.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.468][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:35.470][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:35.471][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.472][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.473][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:35.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:35.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.479][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:35.480][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:35.481][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.483][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.485][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:35.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:35.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:35.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:35.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:35.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:35.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:35.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:35.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.558][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:35.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:35.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:35.583][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2025-03-19 23:20:35.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:35.617][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:35.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:35.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:35.627][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:20:35.633][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:35.635][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:35.638][private$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[2025-03-19 23:20:35.957][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[2025-03-19 23:20:36.280][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:36.284][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-03-19 23:20:36.291][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-03-19 23:20:36.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:36.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:36.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:36.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:36.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:36.349][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:36.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:36.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:36.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:36.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:36.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:36.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:36.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:36.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:36.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:36.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:36.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:36.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:36.376][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:36.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:36.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:36.388][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:36.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:36.391][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:36.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:36.393][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2025-03-19 23:20:36.395][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:36.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2025-03-19 23:20:36.400][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:36.402][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:36.403][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:36.404][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:36.406][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:36.408][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:36.430][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:36.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:36.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:36.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:36.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:36.451][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:36.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:36.455][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2025-03-19 23:20:36.459][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:36.460][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:36.462][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2025-03-19 23:20:36.801][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2025-03-19 23:20:38.124][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:38.129][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2025-03-19 23:20:38.136][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2025-03-19 23:20:38.154][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2025-03-19 23:20:38.159][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:38.162][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:38.165][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:38.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:38.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:38.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:38.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:38.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:38.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:38.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:38.193][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.195][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.199][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.209][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:38.211][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:38.213][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.215][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.218][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:38.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:38.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.226][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:38.228][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:38.230][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.231][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.234][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:38.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:38.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.242][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:38.244][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:38.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.248][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:38.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:38.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.258][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:38.260][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:38.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.264][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:38.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:38.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.274][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:38.276][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:38.278][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.279][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.282][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:38.284][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.286][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.290][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:38.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.298][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:38.300][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:38.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.303][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:38.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:38.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.313][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:38.316][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:38.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.319][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.322][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:38.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:38.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.330][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:38.332][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:38.333][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.335][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.345][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:38.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:38.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.354][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:38.356][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:38.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.359][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.361][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:38.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:38.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:38.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:38.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:38.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:38.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:38.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:38.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:38.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:38.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:38.450][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2025-03-19 23:20:38.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:38.551][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[2025-03-19 23:20:38.558][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:20:38.561][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 23:20:38.564][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:20:38.568][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 23:20:38.583][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:38.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:38.588][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:38.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:38.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:38.610][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:38.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:38.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:38.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:38.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:38.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:38.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:38.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:38.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:38.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:38.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:38.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:38.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:38.665][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2025-03-19 23:20:38.667][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:38.671][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2025-03-19 23:20:38.674][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:38.676][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:38.678][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:38.680][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:38.683][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:38.685][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:38.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:38.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:38.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:38.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:38.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:38.710][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:38.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:38.715][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2025-03-19 23:20:38.720][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:38.722][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:38.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2025-03-19 23:20:39.064][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2025-03-19 23:20:39.388][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:39.391][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2025-03-19 23:20:39.396][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2025-03-19 23:20:39.400][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2025-03-19 23:20:39.402][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:39.404][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:39.405][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:39.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:39.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:39.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:41.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:41.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:41.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:41.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:41.645][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.647][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.649][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.661][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.668][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:41.669][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:41.670][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.672][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.673][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:41.675][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:41.677][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.679][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.681][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:41.683][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:41.685][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.686][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.689][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:41.691][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:41.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.696][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:41.698][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:41.700][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.702][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.704][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:41.706][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.709][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.712][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:41.713][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:41.715][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.717][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.719][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:41.721][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:41.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.725][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.727][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:41.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:41.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.734][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:41.735][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:41.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.739][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.740][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:41.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.746][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:41.747][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:41.748][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.750][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:41.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:41.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:41.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:41.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:41.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:41.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.786][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:41.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:41.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:41.807][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2025-03-19 23:20:41.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.823][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:41.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:41.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:41.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:41.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:41.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:41.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:41.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:41.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:41.875][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:41.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:41.880][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2025-03-19 23:20:41.882][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:41.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2025-03-19 23:20:41.889][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:41.891][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:41.893][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:41.896][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:41.898][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:41.900][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:41.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:41.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:41.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:41.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:41.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:41.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:41.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:41.942][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2025-03-19 23:20:41.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:41.949][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:41.952][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2025-03-19 23:20:42.280][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2025-03-19 23:20:42.619][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:42.623][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2025-03-19 23:20:42.632][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2025-03-19 23:20:42.638][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2025-03-19 23:20:42.641][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:42.644][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:42.646][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:42.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:42.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:42.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:42.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:42.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:42.669][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:42.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:42.687][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.690][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.692][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.694][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.705][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:42.707][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:42.709][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.711][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.714][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:42.716][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:42.718][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.719][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.721][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:42.722][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:42.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.724][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.726][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:42.727][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:42.728][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.730][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.731][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:42.733][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:42.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.737][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:42.738][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.741][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.742][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:42.743][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:42.745][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.746][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.748][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:42.749][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:42.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.752][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.754][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:42.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:42.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.759][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:42.761][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:42.762][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.763][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.764][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:42.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:42.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.772][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:42.774][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:42.776][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.778][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:42.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:42.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:42.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:42.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:42.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:42.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.836][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:42.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:42.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:42.843][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2025-03-19 23:20:42.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.852][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.860][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:42.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:42.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:42.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:42.885][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:42.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:42.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:42.901][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:42.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:42.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:42.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:42.908][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2025-03-19 23:20:42.910][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:42.913][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2025-03-19 23:20:42.916][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:42.918][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:42.920][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:42.922][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:42.924][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:42.926][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:42.929][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:42.930][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:42.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:42.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:42.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:42.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:42.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:42.945][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2025-03-19 23:20:42.948][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:42.950][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:42.951][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2025-03-19 23:20:43.284][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2025-03-19 23:20:43.611][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:43.615][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2025-03-19 23:20:43.622][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2025-03-19 23:20:43.628][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2025-03-19 23:20:43.634][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:43.637][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:43.639][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:43.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:43.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:43.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:43.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:43.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:43.677][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:43.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:43.683][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.685][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.699][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:43.700][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:43.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.703][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.704][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:43.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:43.707][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.708][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.710][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:43.711][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:43.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.714][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.715][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:43.717][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:43.719][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.721][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.723][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:43.725][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:43.727][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.729][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.731][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:43.733][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.737][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.740][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:43.742][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:43.743][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.745][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.747][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:43.749][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:43.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.753][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:43.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:43.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.765][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:43.767][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:43.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.773][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:43.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:43.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.782][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:43.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:43.786][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.787][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:43.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:43.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:43.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:43.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:43.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:43.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.856][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:43.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:43.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:43.880][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2025-03-19 23:20:43.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.899][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:43.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:43.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:43.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:43.923][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:43.925][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:43.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:43.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:43.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:43.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:43.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:43.952][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2025-03-19 23:20:43.954][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:43.957][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2025-03-19 23:20:43.959][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:43.962][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:43.964][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:43.966][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:43.968][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:43.970][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:43.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:43.977][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:43.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:43.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:43.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:43.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:43.998][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[2025-03-19 23:20:44.000][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2025-03-19 23:20:44.003][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:44.005][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:44.006][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2025-03-19 23:20:44.353][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2025-03-19 23:20:44.692][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:44.695][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2025-03-19 23:20:44.700][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2025-03-19 23:20:44.704][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2025-03-19 23:20:44.706][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:44.708][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:44.710][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:44.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:44.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:44.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:44.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:44.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:44.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:44.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:44.757][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.758][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.759][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.760][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.767][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:44.768][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:44.770][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.771][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.772][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:44.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:44.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.778][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:44.779][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:44.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.783][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:44.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:44.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.788][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:44.789][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:44.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:44.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:44.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.799][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:44.800][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:44.801][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.802][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.804][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:44.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:44.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.809][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:44.811][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:44.812][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.813][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.815][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:44.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:44.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.820][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:44.821][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.822][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.823][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.825][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.832][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:44.834][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:44.835][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.837][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:44.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:44.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.848][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:44.850][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:44.852][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.854][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.857][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:44.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:44.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.865][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:44.867][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:44.869][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.880][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:44.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:44.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.886][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:44.888][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:44.889][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.890][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.892][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:44.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:44.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:44.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:44.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:44.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:44.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.912][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:44.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:44.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:44.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:44.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:44.950][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2025-03-19 23:20:44.951][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:44.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:44.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:44.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:44.967][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:44.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:44.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:44.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:44.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:44.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:44.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:44.984][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2025-03-19 23:20:44.985][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:44.987][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2025-03-19 23:20:44.989][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:44.990][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:44.992][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:44.993][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:44.994][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:44.995][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:45.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:45.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:45.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:45.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:45.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:45.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:45.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:45.029][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2025-03-19 23:20:45.033][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:45.034][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:45.036][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2025-03-19 23:20:45.349][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2025-03-19 23:20:45.674][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:45.679][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2025-03-19 23:20:45.686][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2025-03-19 23:20:45.693][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2025-03-19 23:20:45.697][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:45.699][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:45.702][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:45.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:45.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:45.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:45.722][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:45.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:45.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:45.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:45.731][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.734][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.735][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.737][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.748][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:45.750][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:45.751][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.753][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.755][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:45.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:45.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.761][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:45.763][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:45.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.767][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.770][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:45.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:45.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.777][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:45.778][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:45.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.782][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:45.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:45.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.789][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:45.790][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:45.791][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.793][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.794][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:45.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:45.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.802][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:45.804][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:45.806][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.808][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.810][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:45.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:45.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.830][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:45.833][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:45.834][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.836][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.839][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:45.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:45.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.846][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:45.848][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:45.850][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.852][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:45.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:45.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.862][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:45.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:45.866][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.868][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.871][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:45.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:45.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.880][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:45.882][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:45.884][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.886][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.888][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:45.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:45.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.894][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:45.895][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:45.897][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.898][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.899][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:45.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:45.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:45.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:45.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:45.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:45.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:45.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:45.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:45.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:45.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:45.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:45.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:45.962][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2025-03-19 23:20:45.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:45.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:45.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:46.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:46.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:46.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:46.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:46.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:46.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:46.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:46.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:46.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:46.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:46.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:46.181][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2025-03-19 23:20:46.183][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:46.184][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2025-03-19 23:20:46.186][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:46.188][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:46.189][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:46.190][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:46.191][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:46.193][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:46.195][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:46.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:46.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:46.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:46.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:46.207][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:46.208][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[2025-03-19 23:20:46.210][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2025-03-19 23:20:46.213][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:46.214][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:46.216][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2025-03-19 23:20:46.543][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2025-03-19 23:20:46.872][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:46.876][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2025-03-19 23:20:46.883][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2025-03-19 23:20:46.888][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2025-03-19 23:20:46.892][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:46.894][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:46.896][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:46.900][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:46.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:46.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:46.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:46.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:46.919][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:46.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:46.925][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:46.927][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:46.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.931][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:46.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:46.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.942][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:46.944][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:46.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.950][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:46.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:46.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.958][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:46.960][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:46.962][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.964][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.966][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:46.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:46.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.974][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:46.976][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:46.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.980][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:46.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:46.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.990][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:46.992][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:46.994][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:46.996][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:46.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:47.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:47.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.007][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:47.010][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:47.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.014][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.016][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:47.018][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.023][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:47.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.030][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:47.031][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:47.033][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.035][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:47.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:47.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.042][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:47.044][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:47.045][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.048][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:47.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:47.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.055][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:47.056][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:47.058][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.059][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.061][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:47.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:47.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.067][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:47.069][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:47.070][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.071][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.073][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:47.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:47.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:47.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:47.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:47.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:47.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:47.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:47.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:47.147][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2025-03-19 23:20:47.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.164][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:47.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:47.172][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:47.174][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:47.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:47.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:47.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:47.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:47.188][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[2025-03-19 23:20:47.190][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2025-03-19 23:20:47.191][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:47.193][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2025-03-19 23:20:47.195][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:47.197][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:47.198][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:47.200][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:47.202][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:47.203][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:47.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:47.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:47.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:47.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:47.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:47.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:47.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:47.231][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2025-03-19 23:20:47.236][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:47.238][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:47.241][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2025-03-19 23:20:47.554][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2025-03-19 23:20:47.885][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:47.889][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2025-03-19 23:20:47.896][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2025-03-19 23:20:47.901][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2025-03-19 23:20:47.904][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:47.907][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:47.909][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:47.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:47.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:47.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:47.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:47.929][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:47.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:47.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:47.937][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.938][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.940][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.941][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:47.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:47.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.952][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:47.954][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:47.957][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.958][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.960][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:47.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:47.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.969][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:47.971][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:47.973][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.974][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:47.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:47.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.984][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:47.986][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:47.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.989][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.992][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:47.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:47.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:47.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:47.999][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:48.001][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:48.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:48.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:48.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.015][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:48.017][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:48.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.021][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.023][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:48.025][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.027][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.029][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.032][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:48.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.040][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:48.042][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:48.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:48.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:48.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.056][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:48.058][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:48.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:48.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:48.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.071][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:48.073][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:48.074][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.075][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.077][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:48.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:48.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.098][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:48.100][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:48.102][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.104][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.106][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:48.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:48.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:48.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:48.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:48.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:48.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:48.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:48.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:48.190][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2025-03-19 23:20:48.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.201][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:48.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:48.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:48.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:48.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:48.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:48.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:48.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:48.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:48.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:48.239][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2025-03-19 23:20:48.241][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:48.244][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2025-03-19 23:20:48.246][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:48.249][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:48.251][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:48.253][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:48.255][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:48.257][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:48.262][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:48.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:48.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:48.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:48.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:48.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:48.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:48.289][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2025-03-19 23:20:48.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:48.296][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:48.299][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2025-03-19 23:20:48.626][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2025-03-19 23:20:48.937][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:48.942][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2025-03-19 23:20:48.949][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2025-03-19 23:20:48.954][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2025-03-19 23:20:48.958][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:48.960][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:48.963][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:48.966][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:48.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:48.969][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:48.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:48.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:48.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:48.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:48.991][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:48.994][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:48.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:48.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.008][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:49.010][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:49.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.013][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.016][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:49.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:49.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.024][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:49.026][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:49.028][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.030][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.032][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:49.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:49.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.040][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:49.042][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:49.044][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.046][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:49.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:49.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.056][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:49.058][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:49.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.062][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.065][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:49.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:49.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.073][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:49.075][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:49.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.078][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.081][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:49.083][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.085][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.087][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.089][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:49.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.097][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:49.099][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:49.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.105][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:49.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:49.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.114][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:49.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:49.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:49.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:49.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:49.126][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:49.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.130][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:49.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:49.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.137][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:49.138][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:49.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.142][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.144][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:49.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:49.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:49.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:49.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:49.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:49.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.164][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:49.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:49.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:49.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:49.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:49.210][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2025-03-19 23:20:49.211][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:49.222][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:49.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:49.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:49.227][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:49.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:49.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:49.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:49.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:49.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:49.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:49.246][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2025-03-19 23:20:49.247][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:49.250][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2025-03-19 23:20:49.252][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:49.253][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:49.255][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:49.257][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:49.259][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:49.260][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:49.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:49.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:49.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:49.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:49.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:49.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:49.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:49.280][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2025-03-19 23:20:49.285][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:49.287][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:49.290][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2025-03-19 23:20:49.617][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2025-03-19 23:20:49.950][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:49.954][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2025-03-19 23:20:49.961][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2025-03-19 23:20:49.967][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2025-03-19 23:20:49.970][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:49.973][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:49.976][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:49.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:49.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:49.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:49.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:49.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:49.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:49.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:49.999][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.001][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.003][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.005][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.014][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:50.016][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:50.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.022][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:50.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:50.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.031][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:50.033][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:50.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.049][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:50.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:50.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.055][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:50.057][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:50.059][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.060][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:50.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:50.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.069][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:50.071][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:50.073][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.074][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:50.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:50.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:50.083][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:50.084][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.086][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.087][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:50.089][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.090][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.092][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.094][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:50.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:50.103][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:50.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.106][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:50.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:50.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.116][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:50.119][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:50.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.122][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:50.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:50.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.133][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:50.135][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:50.137][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.141][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:50.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:50.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.150][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:50.152][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:50.154][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.155][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.158][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:50.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:50.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:50.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:50.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:50.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:50.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:50.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:50.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:50.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:50.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:50.242][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2025-03-19 23:20:50.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:50.260][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:50.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:50.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:50.268][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:50.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:50.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:50.284][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:50.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:50.287][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:50.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:50.292][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2025-03-19 23:20:50.294][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:50.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2025-03-19 23:20:50.299][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:50.302][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:50.304][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:50.306][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:50.308][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:50.309][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:50.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:50.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:50.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:50.328][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:50.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:50.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:50.333][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[2025-03-19 23:20:50.335][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2025-03-19 23:20:50.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:50.342][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:50.344][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2025-03-19 23:20:50.683][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2025-03-19 23:20:51.017][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:51.020][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2025-03-19 23:20:51.026][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2025-03-19 23:20:51.030][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2025-03-19 23:20:51.033][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:51.035][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:51.036][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:51.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:51.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:51.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:51.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:51.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:51.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:51.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:51.063][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.065][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.067][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.069][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.079][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:51.081][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:51.083][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.085][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.087][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:51.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:51.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.095][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:51.097][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:51.099][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.100][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:51.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.111][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:51.113][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:51.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.117][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.127][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:51.129][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:51.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.133][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:51.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:51.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.143][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:51.145][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:51.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.151][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:51.153][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.157][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.159][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:51.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.167][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:51.169][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:51.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.173][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:51.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:51.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.183][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:51.185][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:51.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.189][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:51.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:51.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.199][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:51.201][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:51.203][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.205][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.207][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:51.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:51.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.215][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:51.217][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:51.218][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.220][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:51.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:51.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:51.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:51.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:51.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:51.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:51.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:51.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:51.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:51.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:51.310][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2025-03-19 23:20:51.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:51.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:51.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:51.331][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:51.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:51.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:51.341][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:51.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:51.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:51.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:51.346][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2025-03-19 23:20:51.347][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:51.349][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2025-03-19 23:20:51.351][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:51.353][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:51.354][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:51.355][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:51.357][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:51.358][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:51.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:51.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:51.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:51.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:51.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:51.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:51.382][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[2025-03-19 23:20:51.383][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2025-03-19 23:20:51.388][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:51.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:51.391][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2025-03-19 23:20:51.722][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2025-03-19 23:20:52.055][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:52.059][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2025-03-19 23:20:52.069][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2025-03-19 23:20:52.074][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2025-03-19 23:20:52.077][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:52.080][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:52.082][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:52.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:52.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:52.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:52.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:52.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:52.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:52.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:52.105][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.107][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.109][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.115][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:52.117][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:52.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.119][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:52.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:52.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.127][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:52.129][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:52.130][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.131][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.133][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:52.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:52.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.139][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:52.140][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:52.141][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.143][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.145][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:52.147][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:52.149][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.150][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.153][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:52.154][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:52.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.158][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.160][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:52.162][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.164][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.165][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.167][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:52.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.175][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:52.176][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:52.178][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.179][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:52.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:52.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.186][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:52.187][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:52.188][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.190][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:52.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:52.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.196][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:52.198][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:52.199][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.200][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.202][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:52.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:52.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.207][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:52.208][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:52.210][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.212][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:52.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:52.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:52.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:52.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:52.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:52.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:52.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:52.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:52.292][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2025-03-19 23:20:52.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.302][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:52.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:52.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:52.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:52.314][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:52.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:52.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:52.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:52.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:52.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:52.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:52.328][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2025-03-19 23:20:52.330][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:52.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2025-03-19 23:20:52.333][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:52.335][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:52.336][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:52.337][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:52.338][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:52.340][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:52.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:52.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:52.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:52.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:52.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:52.356][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:52.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:52.359][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2025-03-19 23:20:52.363][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:52.364][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:52.366][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2025-03-19 23:20:52.682][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2025-03-19 23:20:53.011][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:53.014][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2025-03-19 23:20:53.019][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2025-03-19 23:20:53.023][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2025-03-19 23:20:53.025][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:53.027][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:53.028][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:53.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:53.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:53.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:53.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:53.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:53.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:53.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:53.047][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.048][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.050][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.051][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.057][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:53.058][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:53.060][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.061][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.063][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:53.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:53.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.069][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:53.070][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:53.071][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.073][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:53.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:53.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.079][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:53.080][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:53.082][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.083][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.084][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:53.086][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:53.087][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.088][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.089][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:53.091][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:53.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.093][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.095][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:53.096][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.100][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:53.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.105][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:53.106][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:53.107][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.108][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:53.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:53.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.115][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:53.116][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:53.117][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.118][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:53.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:53.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.125][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:53.126][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:53.128][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.129][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.130][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:53.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:53.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.135][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:53.136][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:53.138][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.139][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:53.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:53.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:53.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:53.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:53.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:53.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.183][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:53.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:53.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:53.194][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2025-03-19 23:20:53.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:53.214][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:53.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:53.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:53.219][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:53.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:53.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:53.229][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:53.230][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:53.232][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:53.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:53.234][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2025-03-19 23:20:53.236][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:53.237][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2025-03-19 23:20:53.239][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:53.241][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:53.242][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:53.243][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:53.244][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:53.246][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:53.248][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:53.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:53.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:53.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:53.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:53.261][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:53.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:53.263][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2025-03-19 23:20:53.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:53.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:53.270][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2025-03-19 23:20:53.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2025-03-19 23:20:53.911][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:53.914][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2025-03-19 23:20:53.918][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2025-03-19 23:20:53.922][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2025-03-19 23:20:53.925][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:53.927][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:53.929][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:53.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:53.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:53.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:56.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:56.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:56.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:56.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:56.156][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.158][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.168][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:56.169][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:56.171][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.172][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.174][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:56.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:56.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.178][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.179][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:56.181][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:56.182][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.183][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.185][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:56.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:56.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.190][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:56.192][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:56.193][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.194][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.196][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:56.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:56.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.201][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:56.202][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:56.204][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.205][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:56.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:56.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.214][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:56.216][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:56.217][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.219][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.221][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:56.223][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.226][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.228][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:56.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.235][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:56.237][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:56.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.240][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:56.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:56.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.249][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:56.251][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:56.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.254][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:56.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:56.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.263][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:56.265][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:56.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.271][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:56.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:56.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.278][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:56.279][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:56.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.283][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.285][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:56.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:56.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:56.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:56.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:56.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:56.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:56.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:56.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:56.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:56.355][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2025-03-19 23:20:56.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:56.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:56.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:56.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:56.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:56.375][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:56.376][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:56.448][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:56.450][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:56.452][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:56.454][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[2025-03-19 23:20:56.457][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2025-03-19 23:20:56.458][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:56.460][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2025-03-19 23:20:56.462][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:56.463][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:56.465][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:56.466][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:56.468][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:56.469][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:56.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:56.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:56.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:56.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:56.483][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:56.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:56.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:56.487][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2025-03-19 23:20:56.491][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:56.492][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:56.494][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2025-03-19 23:20:56.811][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2025-03-19 23:20:57.148][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:57.152][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2025-03-19 23:20:57.160][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2025-03-19 23:20:57.165][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2025-03-19 23:20:57.169][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:57.171][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:57.174][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:57.177][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:57.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:57.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:57.191][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:57.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:57.193][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:57.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:57.198][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.199][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.201][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.202][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.210][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:57.212][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:57.214][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.216][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.219][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:57.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:57.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.228][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:57.230][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:57.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.234][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.236][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:57.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:57.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.245][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:57.247][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:57.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:57.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:57.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.262][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:57.264][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:57.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:57.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:57.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.280][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:57.282][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:57.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.288][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:57.291][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.293][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.297][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:57.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.306][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:57.308][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:57.310][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.312][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:57.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:57.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.324][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:57.326][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:57.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.330][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:57.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:57.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.337][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:57.338][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:57.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.341][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.343][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:57.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:57.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.361][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:57.363][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:57.365][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.367][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.369][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:57.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:57.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:57.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:57.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:57.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:57.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:57.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:57.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.424][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:57.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:57.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:57.454][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2025-03-19 23:20:57.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:57.471][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:57.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:57.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:57.479][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:57.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:57.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:57.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:57.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:57.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:57.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:57.499][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2025-03-19 23:20:57.501][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:57.504][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2025-03-19 23:20:57.507][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:57.509][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:57.511][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:57.513][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:57.515][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:57.517][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:57.521][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:57.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:57.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:57.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:57.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:57.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:57.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:57.545][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2025-03-19 23:20:57.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:57.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:57.554][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2025-03-19 23:20:57.874][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2025-03-19 23:20:58.318][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:58.322][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2025-03-19 23:20:58.329][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2025-03-19 23:20:58.335][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2025-03-19 23:20:58.338][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:58.341][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:58.343][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:58.346][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:58.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:58.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:58.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:58.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:58.458][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:58.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:20:58.464][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.466][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.468][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.470][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.480][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:58.482][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:58.483][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.485][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.487][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:20:58.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:20:58.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.495][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:58.497][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:58.499][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.501][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.503][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:20:58.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:20:58.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.511][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:58.513][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:58.515][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.516][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:20:58.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:20:58.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.526][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:58.528][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:58.530][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.532][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:20:58.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:20:58.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.541][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:58.543][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:20:58.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.548][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:58.551][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.552][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.554][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:20:58.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.564][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:58.567][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:58.569][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.571][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:58.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:20:58.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.582][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:58.584][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:58.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.590][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:20:58.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:20:58.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.598][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:58.600][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:58.602][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.604][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.606][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:20:58.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:20:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.615][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:58.617][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:58.618][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.620][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.623][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:20:58.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:20:58.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:58.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:58.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:58.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:58.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:20:58.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:20:58.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.665][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.685][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:20:58.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:20:58.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:58.700][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2025-03-19 23:20:58.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:20:58.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:20:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:20:58.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:20:58.724][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:58.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:58.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:58.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:58.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:58.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:58.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:20:58.748][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2025-03-19 23:20:58.750][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:20:58.753][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2025-03-19 23:20:58.756][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:20:58.758][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:20:58.761][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:20:58.763][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:20:58.765][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:20:58.767][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:20:58.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:58.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:58.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:58.784][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:58.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:58.786][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:58.787][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[2025-03-19 23:20:58.789][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2025-03-19 23:20:58.792][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:20:58.793][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:20:58.795][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2025-03-19 23:20:59.481][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2025-03-19 23:20:59.804][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:20:59.808][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2025-03-19 23:20:59.812][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2025-03-19 23:20:59.816][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2025-03-19 23:20:59.819][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:20:59.820][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:20:59.822][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:20:59.824][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:20:59.825][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:20:59.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:20:59.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:20:59.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:20:59.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:20:59.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:00.001][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.003][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.007][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.017][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:00.019][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:00.020][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.022][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.024][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:00.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:00.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.031][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:00.033][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:00.034][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.036][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.038][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:00.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:00.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.060][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:00.061][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:00.063][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.064][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:00.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:00.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.071][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:00.073][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:00.075][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.077][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:00.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:00.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.088][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:00.090][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:00.092][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.094][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.097][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:00.099][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.105][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:00.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.114][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:00.116][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:00.118][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.120][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:00.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:00.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.131][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:00.133][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:00.134][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.136][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:00.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:00.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.145][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:00.146][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:00.147][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.149][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:00.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:00.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.157][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:00.158][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:00.160][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.161][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.163][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:00.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:00.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.169][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:00.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:00.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.175][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:00.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:00.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:00.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:00.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:00.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:00.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:00.244][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2025-03-19 23:21:00.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:00.263][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:00.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:00.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:00.269][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:00.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:00.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:00.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:00.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:00.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:00.288][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[2025-03-19 23:21:00.290][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2025-03-19 23:21:00.293][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:21:00.296][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2025-03-19 23:21:00.298][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:21:00.301][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:00.303][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:00.305][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:00.307][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:00.310][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:00.313][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:00.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:00.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:00.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:00.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:00.333][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:00.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:00.337][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2025-03-19 23:21:00.342][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:00.345][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:00.347][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2025-03-19 23:21:00.684][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2025-03-19 23:21:01.027][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:01.032][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2025-03-19 23:21:01.039][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2025-03-19 23:21:01.045][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2025-03-19 23:21:01.047][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:01.049][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:21:01.051][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:01.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:01.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:01.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:01.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:01.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:01.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:01.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:01.262][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.264][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.266][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.268][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.278][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:01.280][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:01.282][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.285][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.287][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:01.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:01.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.296][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:01.298][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:01.300][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.302][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.305][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:01.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:01.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.313][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:01.316][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:01.317][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.319][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:01.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:01.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.330][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:01.332][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:01.334][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.336][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.338][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:01.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:01.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.347][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:01.349][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:01.351][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.353][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.356][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:01.358][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.362][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.364][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:01.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.372][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:01.374][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:01.376][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.378][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:01.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:01.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.389][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:01.391][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:01.393][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.395][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.398][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:01.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:01.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.406][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:01.409][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:01.411][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.412][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.415][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:01.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:01.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.423][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:01.426][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:01.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.432][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:01.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:01.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:01.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:01.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:01.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.457][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:01.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:01.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.481][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.514][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:01.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:01.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:01.522][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2025-03-19 23:21:01.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:01.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:01.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:01.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:01.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:01.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:01.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:01.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:01.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:01.566][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:01.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:01.571][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2025-03-19 23:21:01.573][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:21:01.576][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2025-03-19 23:21:01.578][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:21:01.581][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:01.583][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:01.585][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:01.587][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:01.589][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:01.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:01.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:01.598][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:01.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:01.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:01.624][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:01.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:01.628][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2025-03-19 23:21:01.633][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:01.635][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:01.638][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2025-03-19 23:21:02.000][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2025-03-19 23:21:02.315][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:02.320][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2025-03-19 23:21:02.324][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2025-03-19 23:21:02.328][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2025-03-19 23:21:02.331][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:02.332][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:21:02.334][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:02.336][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:02.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:02.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:02.429][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:02.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:02.433][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:02.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:02.439][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.441][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.443][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.445][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.454][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:02.456][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:02.458][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.459][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.462][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:02.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:02.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.469][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:02.471][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:02.473][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.474][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:02.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.484][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:02.486][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:02.488][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.489][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:02.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:02.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:02.501][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:02.504][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.506][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.508][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:02.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:02.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.516][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:02.518][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:02.520][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.522][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.524][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:02.526][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.528][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.530][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.532][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:02.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.540][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:02.542][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:02.544][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.546][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:02.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:02.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.556][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:02.559][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:02.560][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.562][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:02.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:02.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.573][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:02.575][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:02.577][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.579][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.581][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:02.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:02.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.589][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:02.591][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:02.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.594][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.597][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:02.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:02.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:02.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:02.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:02.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:02.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:02.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:02.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.643][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.651][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:02.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:02.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:02.683][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2025-03-19 23:21:02.685][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:02.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:02.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:02.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:02.709][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:02.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:02.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:02.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:02.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:02.728][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:02.730][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[2025-03-19 23:21:02.732][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2025-03-19 23:21:02.734][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:21:02.737][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2025-03-19 23:21:02.740][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:21:02.742][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:02.745][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:02.747][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:02.749][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:02.750][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:02.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:02.757][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:02.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:02.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:02.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:02.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:02.781][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[2025-03-19 23:21:02.784][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2025-03-19 23:21:02.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:02.792][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:02.795][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2025-03-19 23:21:03.116][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2025-03-19 23:21:03.437][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:03.441][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2025-03-19 23:21:03.448][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2025-03-19 23:21:03.454][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2025-03-19 23:21:03.457][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:03.460][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:21:03.462][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:03.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:03.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:03.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:03.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:03.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:03.484][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:03.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:03.491][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.493][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.495][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.497][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.507][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:03.509][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:03.511][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.513][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.515][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:03.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:03.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.523][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:03.525][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:03.526][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.528][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:03.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:03.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.537][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:03.539][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:03.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:03.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:03.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.554][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:03.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:03.558][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.560][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.562][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:03.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:03.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.571][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:03.573][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:03.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.577][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.579][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:03.582][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.583][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.585][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.588][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:03.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.596][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:03.598][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:03.600][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.602][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:03.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:03.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.611][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:03.613][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:03.615][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.617][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:03.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:03.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.627][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:03.629][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:03.631][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.633][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.635][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:03.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:03.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.643][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:03.645][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:03.647][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.649][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.651][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:03.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:03.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.659][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:03.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:03.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:03.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:03.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:03.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:03.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.688][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.733][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:03.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:03.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:03.738][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2025-03-19 23:21:03.739][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:03.789][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[2025-03-19 23:21:03.795][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:03.798][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 23:21:03.800][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:03.804][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 23:21:03.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:03.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:03.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:03.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:03.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:03.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:03.830][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[2025-03-19 23:21:03.832][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.839][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:03.855][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:03.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:03.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:03.870][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:03.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:03.873][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:03.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:03.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.892][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.900][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:03.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:03.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:03.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:03.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:03.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:03.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:03.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:03.937][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:03.969][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:03.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:03.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:03.977][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:03.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:03.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:03.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:03.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:03.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:03.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.015][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.063][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.110][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[2025-03-19 23:21:04.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.145][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.228][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.256][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.299][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.334][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.342][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.344][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.364][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.TRACE[2025-03-19 23:21:04.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.392][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.416][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.446][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.466][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.501][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.570][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.575][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.576][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.599][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.621][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.632][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:04.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.651][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:04.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:04.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:04.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:04.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:04.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:04.665][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.TRACE[2025-03-19 23:21:04.666][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:04.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:04.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:04.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:04.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:04.757][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[2025-03-19 23:21:04.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:04.762][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:04.765][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:21:05.093][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:21:05.411][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:05.415][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-03-19 23:21:05.423][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-03-19 23:21:05.430][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:05.436][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:05.438][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:05.442][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:21:05.771][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:21:06.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:06.099][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-03-19 23:21:06.106][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-03-19 23:21:06.111][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:06.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:06.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:06.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:06.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:06.126][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:06.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:06.129][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-03-19 23:21:06.130][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:21:06.133][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-03-19 23:21:06.134][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:21:06.136][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:06.137][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:06.138][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:06.139][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:06.141][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:06.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:06.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:06.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:06.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:06.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:06.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:06.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:06.159][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-03-19 23:21:06.162][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:06.164][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:06.165][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-03-19 23:21:06.483][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-03-19 23:21:06.831][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:06.836][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-03-19 23:21:06.842][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-03-19 23:21:06.848][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-03-19 23:21:06.852][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:06.854][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:21:06.857][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:06.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:06.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:06.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:06.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:06.873][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:06.874][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:06.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:06.878][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:06.880][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:06.881][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.882][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:06.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:06.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.888][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:06.898][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:06.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.908][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:06.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:06.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.913][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:06.914][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:06.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.917][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:06.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:06.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.928][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:06.931][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:06.932][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.934][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.937][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:06.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:06.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.944][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:06.945][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:06.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:06.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:06.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.954][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:06.955][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:06.956][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.957][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.959][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:06.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:06.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.963][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:06.965][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:06.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.967][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.968][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:06.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:06.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.973][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:06.975][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:06.976][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.977][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:06.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:06.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.983][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:06.984][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:06.986][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.987][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.993][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:06.995][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:06.996][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:06.997][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:06.998][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:07.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:07.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.003][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:07.004][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:07.005][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.007][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.008][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:07.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:07.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.013][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:07.062][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-03-19 23:21:07.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:07.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:07.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:07.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:07.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:07.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:07.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:07.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:07.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:07.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:07.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:07.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:07.122][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:07.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:07.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:07.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:07.127][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-03-19 23:21:07.128][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:21:07.130][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-03-19 23:21:07.131][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:21:07.133][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:07.134][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:07.135][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:07.137][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:07.138][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:07.141][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:07.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:07.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:07.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:07.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:07.154][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:07.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:07.157][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-03-19 23:21:07.161][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:07.162][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:07.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-03-19 23:21:07.473][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-03-19 23:21:07.799][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:07.803][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-03-19 23:21:07.810][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-03-19 23:21:07.815][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-03-19 23:21:07.818][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:07.821][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:21:07.823][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:07.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:07.828][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:07.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:07.836][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:07.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:07.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:07.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:07.842][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.844][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.845][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.846][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.852][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:07.854][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:07.855][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.857][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.860][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:07.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:07.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.865][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:07.866][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:07.868][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.869][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.871][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:07.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:07.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.877][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:07.878][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:07.880][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.881][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:07.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:07.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.888][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:07.889][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:07.890][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.891][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:07.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:07.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.898][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:07.899][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:07.900][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.901][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.903][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:07.904][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:07.905][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.906][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.908][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:07.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:07.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.913][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.914][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.915][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.916][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:07.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.923][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:07.924][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:07.925][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.926][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.928][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:07.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:07.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.933][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:07.934][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:07.935][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.937][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.938][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:07.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:07.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.943][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:07.944][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:07.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.947][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.948][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:07.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:07.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:07.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:07.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:07.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:07.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:07.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:08.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.003][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-03-19 23:21:08.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.060][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[2025-03-19 23:21:08.064][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:08.066][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 23:21:08.068][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:08.071][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 23:21:08.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.145][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.168][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.182][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.210][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.220][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.237][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.241][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.267][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.298][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.TRACE[2025-03-19 23:21:08.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.338][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.425][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.437][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.451][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.460][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.463][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.465][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.TRACE[2025-03-19 23:21:08.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.473][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.501][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.509][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.518][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.557][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.568][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.570][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.584][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.589][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.593][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.612][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.618][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.638][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.658][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[2025-03-19 23:21:08.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.694][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.696][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.714][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.726][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.743][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.753][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.755][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.774][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.775][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.831][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.834][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.835][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.TRACE[2025-03-19 23:21:08.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.854][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.867][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.868][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[2025-03-19 23:21:08.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.917][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[2025-03-19 23:21:08.921][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:08.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-03-19 23:21:08.926][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:08.929][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-03-19 23:21:08.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.935][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.949][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.950][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[2025-03-19 23:21:08.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:08.972][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:08.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:08.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:08.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:08.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:08.984][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:08.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:08.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:08.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:08.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:08.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.013][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:09.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.062][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:09.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.088][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.102][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.109][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.114][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.135][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.TRACE[2025-03-19 23:21:09.138][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.176][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.179][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:09.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.192][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:09.212][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.236][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.248][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:09.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.282][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:09.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.328][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.330][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.TRACE[2025-03-19 23:21:09.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.341][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:09.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:09.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:09.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:09.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:09.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:09.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:09.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:09.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:09.406][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:09.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:09.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:12.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:12.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:12.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:12.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:12.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.867][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:12.877][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:12.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:12.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:12.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:12.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:12.896][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:12.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:12.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:12.914][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:12.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:12.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:12.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:12.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:12.926][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:12.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:12.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.940][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:12.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:12.946][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:12.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:12.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:12.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:12.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:12.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:12.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:12.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:12.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:12.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:12.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:12.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:12.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:12.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:12.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:12.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:12.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.017][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.038][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.TRACE[2025-03-19 23:21:13.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.078][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.101][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.124][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[2025-03-19 23:21:13.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.131][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.158][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.170][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.205][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:13.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:13.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 23:21:13.227][biodb::testThat]
biodb.INFO [2025-03-19 23:21:13.229][biodb::testThat] Running test function  test_annotateMzValues_input_vector  (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-03-19 23:21:13.232][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:13.234][biodb::testThat]
biodb.TRACE[2025-03-19 23:21:13.240][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 23:21:13.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 23:21:13.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.299][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.300][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.318][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:13.324][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[2025-03-19 23:21:13.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:13.332][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-19 23:21:13.335][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:13.339][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-19 23:21:13.343][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.364][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.TRACE[2025-03-19 23:21:13.367][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.392][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[2025-03-19 23:21:13.398][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:13.401][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-19 23:21:13.403][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:13.407][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-19 23:21:13.411][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:13.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.505][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 23:21:13.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.544][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.552][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.554][private$selectFields]
biodb.TRACE[2025-03-19 23:21:13.556][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:13.558][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:13.560][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.562][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.564][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.566][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.568][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.570][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.572][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.574][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.578][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.580][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.582][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.584][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.586][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.588][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.590][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:13.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.629][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-19 23:21:13.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.645][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.659][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.661][private$selectFields]
biodb.TRACE[2025-03-19 23:21:13.662][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:13.663][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:13.664][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.666][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.667][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.668][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.669][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.670][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.672][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.673][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.674][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.675][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.676][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.678][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.679][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.680][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.681][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.683][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:13.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.700][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 23:21:13.701][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.713][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:13.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.721][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.726][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.727][private$selectFields]
biodb.TRACE[2025-03-19 23:21:13.728][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:13.729][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:13.730][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.731][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.733][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.734][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.735][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.736][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.738][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.739][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.740][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.741][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.742][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:13.743][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.745][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.746][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.747][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.748][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:13.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:13.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.764][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-19 23:21:13.765][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 23:21:13.766][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 23:21:13.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:13.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:13.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:13.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:13.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:13.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:13.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:13.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:13.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:13.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:13.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:13.872][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[2025-03-19 23:21:13.878][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:13.880][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:13.884][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:21:14.203][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:21:14.519][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:14.523][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-03-19 23:21:14.530][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-03-19 23:21:14.536][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:14.542][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:14.544][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:14.547][private$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[2025-03-19 23:21:14.864][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[2025-03-19 23:21:15.188][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:15.191][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-03-19 23:21:15.197][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-03-19 23:21:15.201][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:15.202][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:15.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:15.211][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:15.213][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:15.215][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:15.216][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:15.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:15.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:15.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:15.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:15.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:15.246][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:15.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:15.249][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:15.265][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:15.266][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:15.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:15.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:15.279][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:15.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:15.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:15.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.293][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:15.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:15.347][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 23:21:15.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:15.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:15.391][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:15.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:15.405][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:15.407][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:15.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:15.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.428][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.430][private$selectFields]
biodb.TRACE[2025-03-19 23:21:15.432][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:15.434][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:15.436][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.438][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.440][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.442][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.444][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.446][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.450][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.452][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.454][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.456][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.458][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.460][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.462][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.464][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.466][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:15.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.491][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-19 23:21:15.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:15.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:15.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:15.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:15.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:15.514][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:15.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:15.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.565][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.566][private$selectFields]
biodb.TRACE[2025-03-19 23:21:15.568][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:15.569][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:15.570][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.571][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.575][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.576][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.578][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.580][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.582][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.584][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.586][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.600][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:15.602][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.603][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.604][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.606][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:15.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:15.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:15.623][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 23:21:15.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:15.636][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:15.637][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:15.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:15.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:15.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:15.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:15.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:15.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.007][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.008][private$selectFields]
biodb.TRACE[2025-03-19 23:21:16.009][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:16.010][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:16.011][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.012][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.013][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.015][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.016][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.017][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.018][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.019][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.020][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.022][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.023][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.024][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.025][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.026][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.028][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.029][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:16.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.045][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-19 23:21:16.046][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 23:21:16.047][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 23:21:16.059][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:16.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:16.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 23:21:16.070][biodb::testThat]
biodb.INFO [2025-03-19 23:21:16.072][biodb::testThat] Running test function  test_annotateMzValues_ppm_tol  (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-03-19 23:21:16.073][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:16.074][biodb::testThat]
biodb.TRACE[2025-03-19 23:21:16.078][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 23:21:16.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 23:21:16.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.105][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:16.127][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[2025-03-19 23:21:16.133][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:16.136][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-19 23:21:16.139][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:16.143][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-19 23:21:16.147][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.197][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[2025-03-19 23:21:16.203][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:16.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-19 23:21:16.208][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:16.212][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-19 23:21:16.217][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.237][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.257][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:16.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.288][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 23:21:16.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.303][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[2025-03-19 23:21:16.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.316][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.317][private$selectFields]
biodb.TRACE[2025-03-19 23:21:16.319][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:16.320][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:16.321][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.322][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.324][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.329][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.331][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.332][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.334][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.335][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.336][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.338][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.340][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:16.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.357][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-19 23:21:16.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.371][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.390][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.392][private$selectFields]
biodb.TRACE[2025-03-19 23:21:16.394][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:16.396][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:16.398][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.400][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.402][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.404][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.406][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.408][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.410][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.416][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.418][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.420][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.422][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.424][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.426][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.428][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:16.430][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.453][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 23:21:16.454][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.467][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.480][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.482][private$selectFields]
biodb.TRACE[2025-03-19 23:21:16.484][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:16.485][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:16.487][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.489][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.493][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.495][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.497][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.500][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.502][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.504][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.506][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.508][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.510][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.512][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.514][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.516][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:16.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.545][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-19 23:21:16.548][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 23:21:16.550][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 23:21:16.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.609][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[2025-03-19 23:21:16.613][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[2025-03-19 23:21:16.616][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:16.618][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-19 23:21:16.619][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:16.622][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-19 23:21:16.626][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[2025-03-19 23:21:16.629][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:16.631][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-19 23:21:16.633][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:16.639][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-19 23:21:16.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.655][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[2025-03-19 23:21:16.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.671][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.688][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.718][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.720][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.TRACE[2025-03-19 23:21:16.721][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.726][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:16.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:16.737][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 23:21:16.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.740][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.751][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.759][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.765][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.766][private$selectFields]
biodb.TRACE[2025-03-19 23:21:16.767][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:16.768][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:16.770][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.771][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.772][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.774][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.776][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.777][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.779][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.780][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.781][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.782][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.783][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.784][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.786][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.787][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.788][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.789][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:16.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.806][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-19 23:21:16.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.808][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.820][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:16.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.833][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.834][private$selectFields]
biodb.TRACE[2025-03-19 23:21:16.835][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:16.836][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:16.837][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.839][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.840][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.842][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.843][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.846][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.848][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.849][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.850][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.851][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.853][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.854][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.855][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.856][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:16.858][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.873][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 23:21:16.875][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:16.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:16.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:16.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:16.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:16.892][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:16.893][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.TRACE[2025-03-19 23:21:16.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.908][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.910][private$selectFields]
biodb.TRACE[2025-03-19 23:21:16.912][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:16.914][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:16.916][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.918][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.920][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.922][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.924][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.926][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.929][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.931][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.932][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.935][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.937][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:16.939][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.941][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.943][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.945][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.947][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:16.950][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:16.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:16.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:16.967][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-19 23:21:16.969][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 23:21:16.970][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 23:21:17.034][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:17.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:17.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 23:21:17.046][biodb::testThat]
biodb.INFO [2025-03-19 23:21:17.047][biodb::testThat] Running test function  test_annotateMzValues_input_dataframe_untouched  (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-03-19 23:21:17.048][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:17.050][biodb::testThat]
biodb.TRACE[2025-03-19 23:21:17.054][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-03-19 23:21:17.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-03-19 23:21:17.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.074][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:17.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:17.100][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[2025-03-19 23:21:17.103][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:17.105][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-03-19 23:21:17.107][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:17.109][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-03-19 23:21:17.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.119][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:17.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.137][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:17.148][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[2025-03-19 23:21:17.152][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:17.154][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-03-19 23:21:17.156][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:17.159][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-03-19 23:21:17.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.174][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:17.176][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.181][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:17.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.203][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.204][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[2025-03-19 23:21:17.205][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:17.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:17.221][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 23:21:17.222][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:17.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.249][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.250][private$selectFields]
biodb.TRACE[2025-03-19 23:21:17.251][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:17.252][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:17.253][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.256][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.257][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.258][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.260][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.261][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.262][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.263][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.265][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.267][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.268][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.269][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.272][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.273][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:17.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.289][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2025-03-19 23:21:17.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.303][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:17.306][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.316][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.317][private$selectFields]
biodb.TRACE[2025-03-19 23:21:17.318][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:17.320][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:17.321][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.322][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.323][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.325][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.326][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.327][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.329][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.331][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.332][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.334][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.335][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.336][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.337][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.339][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.340][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:17.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.361][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 23:21:17.362][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.372][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:17.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.768][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.777][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.779][private$selectFields]
biodb.TRACE[2025-03-19 23:21:17.781][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:17.782][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:17.784][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.786][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.788][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.790][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.792][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.794][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.796][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.797][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.799][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.801][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.803][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:17.805][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.807][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.809][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.810][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.812][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:17.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:17.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.838][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2025-03-19 23:21:17.840][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 23:21:17.842][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 23:21:17.881][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:17.905][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.917][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.DEBUG[2025-03-19 23:21:17.920][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[2025-03-19 23:21:17.924][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:17.926][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-03-19 23:21:17.927][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:17.930][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-03-19 23:21:17.934][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[2025-03-19 23:21:17.937][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:17.939][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-03-19 23:21:17.941][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:17.943][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-03-19 23:21:17.946][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:17.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:17.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:17.960][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:17.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:17.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:17.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:17.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:17.988][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:17.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:17.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:18.004][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:18.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:18.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:18.010][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[2025-03-19 23:21:18.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:18.028][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:18.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:18.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:18.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:18.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:18.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:18.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:18.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:18.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:18.063][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-03-19 23:21:18.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:18.066][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:18.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:18.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:18.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:18.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:18.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:18.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.089][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.090][private$selectFields]
biodb.TRACE[2025-03-19 23:21:18.091][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:18.092][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:18.093][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.094][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.096][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.101][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.103][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.104][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.105][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.106][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.107][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.110][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.111][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.127][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-03-19 23:21:18.128][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:18.129][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:18.130][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:18.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:18.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:18.140][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:18.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:18.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.158][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.160][private$selectFields]
biodb.TRACE[2025-03-19 23:21:18.162][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:18.164][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:18.166][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.168][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.170][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.172][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.174][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.175][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.177][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.179][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.181][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.183][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.185][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.187][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.189][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.195][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:18.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.221][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-03-19 23:21:18.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:18.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:18.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:18.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:18.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:18.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:18.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:18.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.264][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.266][private$selectFields]
biodb.TRACE[2025-03-19 23:21:18.267][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-03-19 23:21:18.269][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-03-19 23:21:18.271][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.273][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.275][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.277][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.278][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.282][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.284][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.286][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.288][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.290][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-03-19 23:21:18.291][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.292][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.294][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.295][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.296][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-03-19 23:21:18.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:18.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:18.321][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-03-19 23:21:18.322][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-03-19 23:21:18.324][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-03-19 23:21:18.401][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:18.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-03-19 23:21:18.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:18.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-03-19 23:21:18.415][biodb::testThat]
biodb.INFO [2025-03-19 23:21:18.417][biodb::testThat] Running test function  test.wrong.entry  (" Wrong entry gives NULL ").
biodb.INFO [2025-03-19 23:21:18.419][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:18.421][biodb::testThat]
biodb.DEBUG[2025-03-19 23:21:18.425][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-03-19 23:21:18.427][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:21:18.431][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2025-03-19 23:21:18.433][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:21:18.436][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:18.438][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:18.440][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:18.442][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:18.444][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:18.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:18.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:18.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:18.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:18.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:18.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:18.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:18.473][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-03-19 23:21:18.477][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:18.479][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:18.482][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-03-19 23:21:18.810][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-03-19 23:21:19.130][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:19.135][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-03-19 23:21:19.142][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-03-19 23:21:19.148][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-03-19 23:21:19.151][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:19.154][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:21:19.156][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:19.159][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:19.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:19.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:19.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:19.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:19.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:19.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:19.187][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.189][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.191][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.203][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:19.205][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:19.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.209][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.211][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:19.213][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:19.215][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.217][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:19.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:19.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.225][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.228][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:19.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:19.232][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.234][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.236][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:19.239][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:19.241][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.243][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.245][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:19.247][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:19.249][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.251][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.254][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:19.256][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:19.258][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.260][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.263][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:19.265][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:19.267][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.269][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.272][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:19.274][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:19.276][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.278][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.280][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:19.283][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:19.285][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.287][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.289][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:19.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:19.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:19.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:19.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:19.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:19.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:19.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:19.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:19.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:19.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:19.384][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-03-19 23:21:19.386][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-03-19 23:21:19.422][biodb::testThat]
biodb.INFO [2025-03-19 23:21:19.424][biodb::testThat] Running test function  test.wrong.entry.among.good.ones  (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-03-19 23:21:19.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:19.428][biodb::testThat]
biodb.DEBUG[2025-03-19 23:21:19.470][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-03-19 23:21:19.472][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-03-19 23:21:19.474][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-03-19 23:21:19.477][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-03-19 23:21:19.479][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-03-19 23:21:19.481][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:19.483][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:19.485][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:19.487][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:19.488][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:19.495][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:19.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:19.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:19.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:19.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:19.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:19.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:19.519][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-03-19 23:21:19.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:19.524][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:19.525][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-03-19 23:21:19.849][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-03-19 23:21:20.183][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:20.187][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-03-19 23:21:20.193][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-03-19 23:21:20.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:20.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:20.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:20.213][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:20.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:20.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:20.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:20.219][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-03-19 23:21:20.223][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:20.224][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:20.226][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-03-19 23:21:20.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-03-19 23:21:20.879][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:20.883][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-03-19 23:21:20.890][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-03-19 23:21:20.894][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:20.896][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:20.897][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:20.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:20.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:20.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:20.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:20.912][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-03-19 23:21:20.916][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:20.917][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:20.919][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-03-19 23:21:21.251][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-03-19 23:21:21.565][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:21.570][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-03-19 23:21:21.576][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-03-19 23:21:21.582][private$doSaveContentToFile] Saving to cache [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-03-19 23:21:21.587][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:21.589][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-03-19 23:21:21.590][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:21.592][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:21.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:21.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:21.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:21.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:21.608][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:21.609][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.TRACE[2025-03-19 23:21:21.611][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.613][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.614][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.615][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.622][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:21.623][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:21.624][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.626][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.627][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:21.628][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:21.630][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.631][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.633][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:21.635][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:21.636][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.637][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.639][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:21.641][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:21.643][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.645][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.647][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:21.650][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:21.652][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.654][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.656][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:21.658][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:21.660][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.662][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.665][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:21.667][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:21.669][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.671][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.674][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:21.676][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:21.678][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.680][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.683][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:21.685][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:21.687][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.689][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.692][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:21.694][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:21.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.698][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:21.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:21.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:21.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:21.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:21.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:21.783][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:21.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:21.790][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.792][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.796][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.806][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:21.808][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:21.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.812][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.814][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:21.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:21.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.822][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:21.824][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:21.826][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.828][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.831][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:21.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:21.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.839][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:21.841][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:21.843][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.845][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:21.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:21.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.855][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:21.857][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:21.859][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.861][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.864][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:21.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:21.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.872][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:21.874][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:21.876][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.878][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.880][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:21.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:21.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.889][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:21.891][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:21.893][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.895][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.898][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:21.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:21.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.906][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:21.908][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:21.910][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.912][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.915][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:21.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:21.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.925][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:21.927][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:21.929][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.931][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.934][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:21.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:21.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.942][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:21.945][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:21.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.948][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.951][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:21.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:21.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.959][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:21.961][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:21.963][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.965][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.967][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:21.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:21.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:21.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:21.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:21.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:21.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:21.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:22.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:22.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:22.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:22.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:22.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:22.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:22.071][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.TRACE[2025-03-19 23:21:22.075][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.078][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.079][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.081][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.092][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:22.094][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:22.096][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.098][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.100][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:22.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:22.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.108][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:22.110][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:22.112][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.113][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.116][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:22.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:22.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.124][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:22.125][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:22.127][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.128][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:22.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:22.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.138][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:22.139][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:22.140][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.141][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:22.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:22.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.150][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:22.151][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:22.153][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.154][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.155][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:22.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:22.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.160][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:22.162][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:22.163][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.164][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.166][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:22.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:22.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.171][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:22.173][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:22.175][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.177][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:22.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:22.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.188][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:22.190][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:22.192][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.193][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:22.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:22.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.204][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:22.206][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:22.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.210][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.212][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:22.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:22.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.220][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:22.222][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:22.224][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.226][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.228][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:22.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:22.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:22.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:22.357][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:22.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:22.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:22.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:22.366][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-03-19 23:21:22.367][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-03-19 23:21:22.369][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-03-19 23:21:22.401][biodb::testThat]
biodb.INFO [2025-03-19 23:21:22.403][biodb::testThat] Running test function  test.peak.table  (" The peak table is correct. ").
biodb.INFO [2025-03-19 23:21:22.406][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:22.408][biodb::testThat]
biodb.INFO [2025-03-19 23:21:22.448][biodb::testThat]
biodb.INFO [2025-03-19 23:21:22.450][biodb::testThat] Running test function  test.nb.entries  (" Nb entries is positive. ").
biodb.INFO [2025-03-19 23:21:22.452][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:22.454][biodb::testThat]
biodb.INFO [2025-03-19 23:21:22.472][biodb::testThat]
biodb.INFO [2025-03-19 23:21:22.474][biodb::testThat] Running test function  test.entry.ids  (" We can get a list of entry ids. ").
biodb.INFO [2025-03-19 23:21:22.476][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:22.478][biodb::testThat]
biodb.DEBUG[2025-03-19 23:21:22.483][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[2025-03-19 23:21:22.490][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:22.492][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:22.495][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:21:22.874][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:21:23.307][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:23.312][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-03-19 23:21:23.320][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-03-19 23:21:23.343][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:23.345][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:23.346][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:23.348][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:23.350][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:23.352][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:23.354][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:23.356][ef$get] fields variable is a list.
biodb.INFO [2025-03-19 23:21:23.360][biodb::testThat]
biodb.INFO [2025-03-19 23:21:23.362][biodb::testThat] Running test function  test.annotateMzValues  (" annotateMzValues() works correctly. ").
biodb.INFO [2025-03-19 23:21:23.364][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:23.366][biodb::testThat]
biodb.ERROR[2025-03-19 23:21:23.392][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-03-19 23:21:23.415][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-03-19 23:21:23.444][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 23:21:23.447][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 23:21:23.450][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 23:21:23.452][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 23:21:23.454][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:23.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:23.458][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.462][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 23:21:23.480][biodb::testContext]
biodb.INFO [2025-03-19 23:21:23.482][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:21:23.484][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-03-19 23:21:23.486][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:21:23.488][biodb::testContext]
biodb.INFO [2025-03-19 23:21:23.493][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:21:23.496][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 23:21:23.506][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:23.508][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 23:21:23.510][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 23:21:23.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.516][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[2025-03-19 23:21:23.518][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 23:21:23.520][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 23:21:23.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.528][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 23:21:23.530][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 23:21:23.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.549][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 23:21:23.551][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 23:21:23.554][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 23:21:23.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.559][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 23:21:23.561][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 23:21:23.563][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 23:21:23.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.566][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.DEBUG[2025-03-19 23:21:23.568][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 23:21:23.570][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 23:21:23.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.576][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 23:21:23.577][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 23:21:23.579][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 23:21:23.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.586][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 23:21:23.589][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 23:21:23.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.592][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.597][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 23:21:23.599][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 23:21:23.601][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 23:21:23.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.608][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:21:23.610][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 23:21:23.612][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 23:21:23.614][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 23:21:23.616][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 23:21:23.618][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 23:21:23.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.626][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 23:21:23.628][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 23:21:23.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.635][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 23:21:23.637][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 23:21:23.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.641][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.645][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 23:21:23.647][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 23:21:23.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.653][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[2025-03-19 23:21:23.655][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 23:21:23.657][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 23:21:23.659][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.665][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 23:21:23.667][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 23:21:23.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.675][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:21:23.677][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 23:21:23.682][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 23:21:23.684][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.689][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 23:21:23.690][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 23:21:23.692][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 23:21:23.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.696][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[2025-03-19 23:21:23.699][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 23:21:23.702][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.704][self$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[2025-03-19 23:21:23.706][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.707][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:23.709][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.710][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.711][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.713][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.714][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:21:23.717][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:23.719][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.721][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 23:21:23.723][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:23.725][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.726][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.728][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:23.728][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:23.728][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:23.728][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:21:23.728][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:21:23.730][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:23.732][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.734][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.736][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:23.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.740][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.742][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.744][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.746][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:23.748][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:23.750][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.752][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.755][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 23:21:23.758][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.760][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:21:23.762][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.765][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:23.767][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.769][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.771][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.773][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.775][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:21:23.777][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:23.779][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.781][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 23:21:23.783][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:23.785][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.787][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.789][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:23.789][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:23.789][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:23.789][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:21:23.789][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:21:23.791][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:23.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.795][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.797][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:23.799][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.803][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.805][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.807][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:23.808][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:23.810][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.812][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.815][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 23:21:23.818][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.820][self$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[2025-03-19 23:21:23.823][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.825][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:23.827][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.829][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.831][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.833][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.835][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:21:23.837][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:23.840][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.842][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 23:21:23.844][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:23.846][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.848][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.850][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.852][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:23.854][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.856][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.858][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:23.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.864][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.866][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.867][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:23.869][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:23.870][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.872][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.874][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 23:21:23.877][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.879][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:21:23.881][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.883][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:23.885][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.887][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.889][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.891][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.893][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:21:23.895][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:23.897][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.899][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 23:21:23.900][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:23.902][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.904][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:23.906][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.908][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:23.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.914][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:23.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:23.918][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:23.920][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:23.922][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.924][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:23.925][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:23.927][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:23.928][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:23.931][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:23.932][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.951][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.962][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.971][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:23.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:23.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:23.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:23.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:23.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.048][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.061][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[2025-03-19 23:21:24.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.071][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[2025-03-19 23:21:24.073][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 23:21:24.076][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 23:21:24.078][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 23:21:24.081][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 23:21:24.084][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:21:24.087][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 23:21:24.090][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 23:21:24.092][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 23:21:24.095][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 23:21:24.098][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 23:21:24.100][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:21:24.103][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 23:21:24.106][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 23:21:24.109][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 23:21:24.111][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 23:21:24.114][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 23:21:24.117][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 23:21:24.119][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 23:21:24.122][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:21:24.125][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 23:21:24.128][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 23:21:24.132][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 23:21:24.135][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 23:21:24.138][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 23:21:24.141][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 23:21:24.144][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 23:21:24.147][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 23:21:24.149][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 23:21:24.152][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 23:21:24.155][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 23:21:24.158][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 23:21:24.160][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 23:21:24.163][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 23:21:24.166][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 23:21:24.169][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 23:21:24.171][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 23:21:24.174][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 23:21:24.176][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 23:21:24.179][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 23:21:24.182][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 23:21:24.185][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 23:21:24.198][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 23:21:24.201][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 23:21:24.204][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 23:21:24.207][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 23:21:24.210][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 23:21:24.212][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 23:21:24.215][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 23:21:24.218][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 23:21:24.221][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 23:21:24.224][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 23:21:24.227][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 23:21:24.230][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 23:21:24.232][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 23:21:24.235][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 23:21:24.238][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 23:21:24.240][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 23:21:24.243][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 23:21:24.246][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 23:21:24.248][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 23:21:24.251][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 23:21:24.253][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 23:21:24.256][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 23:21:24.259][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 23:21:24.261][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 23:21:24.264][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 23:21:24.266][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:21:24.269][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:21:24.272][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 23:21:24.274][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 23:21:24.277][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 23:21:24.279][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 23:21:24.282][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 23:21:24.285][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 23:21:24.287][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 23:21:24.288][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 23:21:24.290][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 23:21:24.292][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 23:21:24.295][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 23:21:24.297][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 23:21:24.300][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 23:21:24.303][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 23:21:24.305][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 23:21:24.308][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 23:21:24.312][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:21:24.314][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:24.319][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.323][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.325][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[2025-03-19 23:21:24.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.352][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[2025-03-19 23:21:24.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.392][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.439][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.464][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.471][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.508][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[2025-03-19 23:21:24.510][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.521][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[2025-03-19 23:21:24.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.530][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:24.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:24.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:24.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:24.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:24.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:24.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:24.551][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 23:21:24.555][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 23:21:24.558][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:24.560][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 23:21:24.562][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:24.564][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:24.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:24.568][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:24.570][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:24.572][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 23:21:24.574][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 23:21:24.576][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:24.578][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:24.580][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 23:21:24.582][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 23:21:24.584][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 23:21:24.586][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:24.588][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:24.588][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:24.588][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:24.590][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 23:21:24.592][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:24.594][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:24.597][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:24.598][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:24.600][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:24.602][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:24.604][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:24.604][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 23:21:24.606][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:24.608][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:24.610][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:24.612][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 23:21:24.612][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 23:21:24.615][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:21:24.618][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:21:24.622][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 23:21:24.624][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:21:24.627][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:21:24.630][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:21:24.636][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 23:21:24.638][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 23:21:24.640][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 23:21:24.644][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 23:21:24.646][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:21:24.648][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:21:24.651][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 23:21:24.653][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 23:21:24.656][biodb::testThat]
biodb.INFO [2025-03-19 23:21:24.658][biodb::testThat] Running test function  test_chebi_convCasToChebi  (" convCasToChebi() works. ").
biodb.INFO [2025-03-19 23:21:24.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:24.662][biodb::testThat]
biodb.DEBUG[2025-03-19 23:21:24.668][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 23:21:24.676][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:24.679][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-19 23:21:24.682][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:24.686][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-19 23:21:24.693][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:24.699][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:24.701][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:24.704][private$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[2025-03-19 23:21:25.028][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[2025-03-19 23:21:25.353][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:25.358][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-03-19 23:21:25.365][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-03-19 23:21:25.370][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:25.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:25.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:26.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:26.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:26.842][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:26.843][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[2025-03-19 23:21:26.846][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[2025-03-19 23:21:26.851][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:26.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:26.856][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:21:27.171][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:21:27.581][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:27.584][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-03-19 23:21:27.591][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-03-19 23:21:27.595][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:27.597][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:27.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:27.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:27.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:27.625][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:27.627][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[2025-03-19 23:21:27.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:27.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:27.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:27.670][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:27.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:27.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:27.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:27.687][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:27.692][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:27.694][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-19 23:21:27.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:27.715][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-19 23:21:27.719][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:27.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:27.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:27.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:27.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:27.735][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:27.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:27.740][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:27.744][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:27.746][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-19 23:21:27.747][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:27.750][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-19 23:21:27.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:27.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:27.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:27.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:27.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:27.771][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:27.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:27.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:27.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:27.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:27.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:27.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:27.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:27.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:27.797][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:27.803][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:27.806][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-03-19 23:21:27.808][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:27.813][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-03-19 23:21:27.816][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:27.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:27.820][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:27.829][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:27.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:27.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:27.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:27.835][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:27.840][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:27.842][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-03-19 23:21:27.844][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:27.847][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-03-19 23:21:27.849][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:27.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:27.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:27.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:27.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:27.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:27.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:27.874][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:27.879][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:27.881][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:27.885][private$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[2025-03-19 23:21:28.211][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[2025-03-19 23:21:28.538][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:28.542][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-03-19 23:21:28.550][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-03-19 23:21:28.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:28.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:28.567][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:28.582][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:28.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:28.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:28.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 23:21:28.601][biodb::testThat]
biodb.INFO [2025-03-19 23:21:28.603][biodb::testThat] Running test function  test_chebi_convInchiToChebi  (" convInchiToChebi() works. ").
biodb.INFO [2025-03-19 23:21:28.604][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:28.605][biodb::testThat]
biodb.DEBUG[2025-03-19 23:21:28.609][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[2025-03-19 23:21:28.613][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:28.614][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:28.616][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:21:28.922][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:21:29.233][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:29.237][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-03-19 23:21:29.246][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-03-19 23:21:29.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:29.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:29.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:29.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:29.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:29.267][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:29.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:29.273][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:29.277][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:29.278][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:29.281][private$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[2025-03-19 23:21:29.598][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[2025-03-19 23:21:29.922][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:29.927][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-03-19 23:21:29.939][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-03-19 23:21:29.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:29.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:29.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:29.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:29.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:29.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:29.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 23:21:29.977][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 23:21:29.979][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 23:21:29.981][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 23:21:29.983][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 23:21:29.985][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:29.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:29.988][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:29.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:29.992][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:29.993][FUN] Functions in observer BiodbConfig: [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 [2025-03-19 23:21:30.001][biodb::testContext]
biodb.INFO [2025-03-19 23:21:30.003][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:21:30.005][biodb::testContext] Test context - Test web services
biodb.INFO [2025-03-19 23:21:30.007][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:21:30.009][biodb::testContext]
biodb.INFO [2025-03-19 23:21:30.013][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:21:30.017][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 23:21:30.025][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:30.027][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 23:21:30.029][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 23:21:30.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.037][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 23:21:30.039][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 23:21:30.041][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.046][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 23:21:30.048][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 23:21:30.050][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.055][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 23:21:30.057][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 23:21:30.059][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 23:21:30.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.065][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 23:21:30.067][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 23:21:30.069][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 23:21:30.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.076][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 23:21:30.078][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 23:21:30.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.085][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 23:21:30.087][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 23:21:30.089][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 23:21:30.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.095][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 23:21:30.097][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 23:21:30.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.105][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 23:21:30.107][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 23:21:30.109][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 23:21:30.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.115][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:21:30.116][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 23:21:30.118][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 23:21:30.119][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 23:21:30.120][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 23:21:30.121][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 23:21:30.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.127][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[2025-03-19 23:21:30.129][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 23:21:30.131][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 23:21:30.133][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.138][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 23:21:30.140][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 23:21:30.142][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.146][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[2025-03-19 23:21:30.148][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 23:21:30.150][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 23:21:30.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.158][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 23:21:30.160][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 23:21:30.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.167][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 23:21:30.170][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 23:21:30.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.177][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:21:30.179][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 23:21:30.185][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 23:21:30.187][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.193][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 23:21:30.195][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 23:21:30.197][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 23:21:30.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.205][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 23:21:30.208][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.210][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-03-19 23:21:30.213][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.215][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:30.217][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.219][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.221][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.223][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.225][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:21:30.227][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:30.229][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.231][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 23:21:30.233][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:30.235][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.237][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.239][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:30.239][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:30.239][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:30.239][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:21:30.239][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:21:30.241][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:30.244][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.245][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.247][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:30.250][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.252][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.253][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.255][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.257][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:30.259][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:30.261][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.263][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.265][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 23:21:30.269][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.271][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:21:30.273][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.275][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:30.277][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.281][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.282][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.284][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:21:30.286][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:30.288][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.290][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 23:21:30.292][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:30.294][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.296][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.307][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:30.307][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:30.307][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:30.307][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:21:30.307][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:21:30.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:30.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.320][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:30.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.325][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.327][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.329][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:30.330][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:30.332][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.334][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.336][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 23:21:30.339][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.342][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-03-19 23:21:30.344][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.346][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:30.348][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.349][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.351][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.353][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.355][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:21:30.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:30.359][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.361][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 23:21:30.363][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:30.364][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.366][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.368][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.370][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:30.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.375][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:30.377][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.379][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.380][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.382][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:30.386][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:30.388][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.389][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.391][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 23:21:30.394][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.396][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:21:30.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:30.402][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.404][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.406][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.410][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:21:30.412][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:30.413][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.415][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 23:21:30.416][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:30.417][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.418][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:30.420][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.421][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:30.422][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.424][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.426][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:30.427][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:30.428][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:30.429][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:30.430][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.432][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:30.433][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:30.435][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:30.436][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:30.439][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:30.440][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.442][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[2025-03-19 23:21:30.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.488][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.496][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.501][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[2025-03-19 23:21:30.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.528][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[2025-03-19 23:21:30.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.537][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[2025-03-19 23:21:30.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.542][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.545][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[2025-03-19 23:21:30.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.554][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[2025-03-19 23:21:30.555][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.566][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.573][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.581][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[2025-03-19 23:21:30.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.590][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[2025-03-19 23:21:30.592][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 23:21:30.594][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 23:21:30.597][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 23:21:30.600][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 23:21:30.602][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:21:30.605][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 23:21:30.608][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 23:21:30.610][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 23:21:30.613][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 23:21:30.616][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 23:21:30.619][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:21:30.621][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 23:21:30.624][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 23:21:30.627][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 23:21:30.629][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 23:21:30.632][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 23:21:30.635][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 23:21:30.637][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 23:21:30.640][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:21:30.643][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 23:21:30.646][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 23:21:30.648][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 23:21:30.651][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 23:21:30.654][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 23:21:30.657][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 23:21:30.659][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 23:21:30.662][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 23:21:30.665][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 23:21:30.667][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 23:21:30.670][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 23:21:30.672][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 23:21:30.675][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 23:21:30.677][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 23:21:30.679][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 23:21:30.682][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 23:21:30.684][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 23:21:30.687][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 23:21:30.689][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 23:21:30.692][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 23:21:30.694][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 23:21:30.697][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 23:21:30.699][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 23:21:30.702][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 23:21:30.704][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 23:21:30.707][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 23:21:30.709][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 23:21:30.712][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 23:21:30.715][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 23:21:30.717][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 23:21:30.720][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 23:21:30.722][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 23:21:30.724][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 23:21:30.725][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 23:21:30.727][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 23:21:30.729][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 23:21:30.731][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 23:21:30.732][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 23:21:30.734][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 23:21:30.736][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 23:21:30.738][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 23:21:30.740][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 23:21:30.743][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 23:21:30.746][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 23:21:30.749][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 23:21:30.751][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 23:21:30.753][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 23:21:30.755][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:21:30.756][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:21:30.758][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 23:21:30.760][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 23:21:30.762][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 23:21:30.765][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 23:21:30.767][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 23:21:30.770][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 23:21:30.772][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 23:21:30.775][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 23:21:30.777][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 23:21:30.780][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 23:21:30.783][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 23:21:30.785][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 23:21:30.788][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 23:21:30.790][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 23:21:30.793][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 23:21:30.796][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 23:21:30.799][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:21:30.801][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:30.803][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.806][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.808][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.DEBUG[2025-03-19 23:21:30.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.815][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.860][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.876][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[2025-03-19 23:21:30.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.901][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.921][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.932][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[2025-03-19 23:21:30.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.946][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.949][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.956][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.DEBUG[2025-03-19 23:21:30.958][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:30.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:30.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:30.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:30.994][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:30.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:30.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:30.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:31.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:31.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:31.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:31.007][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:31.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:31.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:31.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:31.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:31.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:31.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:31.021][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 23:21:31.024][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 23:21:31.027][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:31.029][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 23:21:31.031][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:31.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:31.035][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:31.037][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:31.039][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:31.041][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 23:21:31.043][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 23:21:31.045][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:31.047][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:31.049][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 23:21:31.050][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 23:21:31.052][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 23:21:31.055][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:31.057][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:31.057][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:31.057][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:31.059][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 23:21:31.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:31.062][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:31.064][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:31.066][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:31.067][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:31.069][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:31.071][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:31.071][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 23:21:31.073][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:31.074][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:31.076][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:31.077][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 23:21:31.077][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 23:21:31.079][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:21:31.082][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:21:31.084][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 23:21:31.087][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:21:31.088][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:21:31.090][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:21:31.094][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 23:21:31.095][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 23:21:31.097][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 23:21:31.098][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 23:21:31.100][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:21:31.101][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:21:31.103][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 23:21:31.104][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 23:21:31.106][biodb::testThat]
biodb.INFO [2025-03-19 23:21:31.107][biodb::testThat] Running test function  test.chebi.wsGetLiteEntity  (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-03-19 23:21:31.108][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:31.109][biodb::testThat]
biodb.DEBUG[2025-03-19 23:21:31.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 23:21:31.119][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:31.121][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-19 23:21:31.124][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:31.128][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-19 23:21:31.135][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[2025-03-19 23:21:31.141][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:31.143][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:31.146][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-03-19 23:21:31.767][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-03-19 23:21:32.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:32.099][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-03-19 23:21:32.106][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-03-19 23:21:32.125][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 23:21:32.127][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 23:21:32.130][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 23:21:32.132][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 23:21:32.134][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.137][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.141][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-03-19 23:21:32.151][biodb::testContext]
biodb.INFO [2025-03-19 23:21:32.153][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:21:32.156][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-03-19 23:21:32.158][biodb::testContext] ********************************************************************************
biodb.INFO [2025-03-19 23:21:32.160][biodb::testContext]
biodb.INFO [2025-03-19 23:21:32.164][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:21:32.168][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-03-19 23:21:32.177][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:32.179][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-03-19 23:21:32.181][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-03-19 23:21:32.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.189][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-03-19 23:21:32.191][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-03-19 23:21:32.192][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.197][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-03-19 23:21:32.199][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-03-19 23:21:32.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.206][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-03-19 23:21:32.208][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-03-19 23:21:32.210][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-03-19 23:21:32.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.217][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-03-19 23:21:32.219][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-03-19 23:21:32.221][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-03-19 23:21:32.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.227][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-03-19 23:21:32.229][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-03-19 23:21:32.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.236][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-03-19 23:21:32.238][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-03-19 23:21:32.240][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-03-19 23:21:32.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.247][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-03-19 23:21:32.249][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-03-19 23:21:32.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.254][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.256][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-03-19 23:21:32.258][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-03-19 23:21:32.260][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-03-19 23:21:32.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.265][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.DEBUG[2025-03-19 23:21:32.267][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:21:32.268][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-03-19 23:21:32.270][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-03-19 23:21:32.272][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-03-19 23:21:32.274][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-03-19 23:21:32.276][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-03-19 23:21:32.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.283][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-03-19 23:21:32.285][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-03-19 23:21:32.287][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.290][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[2025-03-19 23:21:32.292][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-03-19 23:21:32.294][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-03-19 23:21:32.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.301][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-03-19 23:21:32.303][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-03-19 23:21:32.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.309][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-03-19 23:21:32.311][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-03-19 23:21:32.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.318][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-03-19 23:21:32.320][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-03-19 23:21:32.322][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.325][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[2025-03-19 23:21:32.327][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-03-19 23:21:32.329][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-03-19 23:21:32.335][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-03-19 23:21:32.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.339][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.340][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-03-19 23:21:32.341][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-03-19 23:21:32.343][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-03-19 23:21:32.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.346][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[2025-03-19 23:21:32.348][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-03-19 23:21:32.350][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.351][self$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[2025-03-19 23:21:32.352][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.353][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:32.355][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.356][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.357][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.359][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.360][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:21:32.361][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:32.363][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.364][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-03-19 23:21:32.365][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:32.367][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.368][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.369][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:32.369][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:32.369][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:32.369][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:21:32.369][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:21:32.370][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:32.372][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.373][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.374][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:32.375][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.378][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.379][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.380][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:32.381][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:32.383][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.384][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.386][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-03-19 23:21:32.388][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.390][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:21:32.391][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.393][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:32.394][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.395][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.397][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.398][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.399][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:21:32.401][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:32.403][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.404][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-03-19 23:21:32.406][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:32.407][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.408][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.410][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:32.410][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:32.410][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:32.410][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-03-19 23:21:32.410][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-03-19 23:21:32.411][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:32.412][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.413][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.415][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:32.416][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.417][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.418][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.419][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.420][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:32.421][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:32.423][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.424][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.425][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-03-19 23:21:32.427][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.429][self$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[2025-03-19 23:21:32.430][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.431][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:32.433][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.434][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.435][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.436][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.437][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-03-19 23:21:32.439][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:32.440][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.441][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-03-19 23:21:32.442][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:32.444][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.445][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.456][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.457][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:32.459][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.460][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.461][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:32.462][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.463][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.464][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.466][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.467][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:32.468][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:32.469][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.470][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.472][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-03-19 23:21:32.474][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.475][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-03-19 23:21:32.476][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.477][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:32.479][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.480][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.481][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.482][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.484][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-03-19 23:21:32.485][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:32.486][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.487][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-03-19 23:21:32.489][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:32.490][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.491][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:32.492][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.494][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-03-19 23:21:32.495][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.496][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.497][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:32.498][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:32.499][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:32.500][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:32.502][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.503][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:32.504][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:32.505][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:32.506][self$setPropertyValue]
biodb.DEBUG[2025-03-19 23:21:32.508][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:32.509][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.516][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[2025-03-19 23:21:32.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.564][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.566][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.568][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.571][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.577][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.581][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[2025-03-19 23:21:32.583][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.590][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.608][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[2025-03-19 23:21:32.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.615][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.627][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-03-19 23:21:32.629][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-03-19 23:21:32.631][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-03-19 23:21:32.633][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-03-19 23:21:32.635][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:21:32.637][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-03-19 23:21:32.638][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-03-19 23:21:32.640][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-03-19 23:21:32.642][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-03-19 23:21:32.644][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-03-19 23:21:32.645][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:21:32.647][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-03-19 23:21:32.649][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-03-19 23:21:32.651][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-03-19 23:21:32.652][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-03-19 23:21:32.654][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-03-19 23:21:32.656][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-03-19 23:21:32.657][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-03-19 23:21:32.659][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:21:32.660][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-03-19 23:21:32.662][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-03-19 23:21:32.664][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-03-19 23:21:32.665][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-03-19 23:21:32.667][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-03-19 23:21:32.668][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-03-19 23:21:32.670][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-03-19 23:21:32.672][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-03-19 23:21:32.673][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-03-19 23:21:32.675][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-03-19 23:21:32.677][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-03-19 23:21:32.679][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-03-19 23:21:32.682][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-03-19 23:21:32.683][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-03-19 23:21:32.685][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-03-19 23:21:32.687][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-03-19 23:21:32.688][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-03-19 23:21:32.690][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-03-19 23:21:32.692][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-03-19 23:21:32.693][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-03-19 23:21:32.695][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-03-19 23:21:32.696][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-03-19 23:21:32.698][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-03-19 23:21:32.699][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-03-19 23:21:32.701][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-03-19 23:21:32.703][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-03-19 23:21:32.704][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-03-19 23:21:32.706][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-03-19 23:21:32.708][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-03-19 23:21:32.709][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-03-19 23:21:32.711][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-03-19 23:21:32.712][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-03-19 23:21:32.714][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-03-19 23:21:32.716][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-03-19 23:21:32.717][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-03-19 23:21:32.719][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-03-19 23:21:32.720][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-03-19 23:21:32.722][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-03-19 23:21:32.724][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-03-19 23:21:32.725][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-03-19 23:21:32.727][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-03-19 23:21:32.729][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-03-19 23:21:32.730][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-03-19 23:21:32.732][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-03-19 23:21:32.733][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-03-19 23:21:32.735][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-03-19 23:21:32.737][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-03-19 23:21:32.739][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:21:32.741][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:21:32.743][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-03-19 23:21:32.746][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-03-19 23:21:32.748][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-03-19 23:21:32.750][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-03-19 23:21:32.753][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-03-19 23:21:32.755][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-03-19 23:21:32.757][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-03-19 23:21:32.759][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-03-19 23:21:32.761][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-03-19 23:21:32.764][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-03-19 23:21:32.766][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-03-19 23:21:32.768][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-03-19 23:21:32.770][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-03-19 23:21:32.773][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-03-19 23:21:32.775][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-03-19 23:21:32.777][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-03-19 23:21:32.780][initialize] This is biodb version 1.15.0.
biodb.DEBUG[2025-03-19 23:21:32.782][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-03-19 23:21:32.784][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.787][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.788][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[2025-03-19 23:21:32.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.799][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[2025-03-19 23:21:32.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.803][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.850][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.860][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[2025-03-19 23:21:32.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.866][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.873][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[2025-03-19 23:21:32.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.889][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.898][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[2025-03-19 23:21:32.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.909][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[2025-03-19 23:21:32.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.955][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.957][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[2025-03-19 23:21:32.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.967][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[2025-03-19 23:21:32.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.973][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.979][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-03-19 23:21:32.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:32.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:32.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:32.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:32.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:32.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:32.997][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-03-19 23:21:33.001][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-03-19 23:21:33.004][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:33.006][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-03-19 23:21:33.008][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:33.010][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-03-19 23:21:33.012][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:33.014][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-03-19 23:21:33.016][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:33.018][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-03-19 23:21:33.020][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-03-19 23:21:33.022][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-03-19 23:21:33.023][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:33.024][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-03-19 23:21:33.026][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-03-19 23:21:33.027][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-03-19 23:21:33.029][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-03-19 23:21:33.030][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-03-19 23:21:33.030][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-03-19 23:21:33.030][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-03-19 23:21:33.031][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-03-19 23:21:33.032][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:33.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:33.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-03-19 23:21:33.036][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-03-19 23:21:33.037][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-03-19 23:21:33.038][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-03-19 23:21:33.039][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:33.039][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-03-19 23:21:33.041][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-03-19 23:21:33.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-03-19 23:21:33.043][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-03-19 23:21:33.045][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-03-19 23:21:33.045][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-03-19 23:21:33.046][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-03-19 23:21:33.048][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-03-19 23:21:33.050][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-03-19 23:21:33.052][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-03-19 23:21:33.054][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-03-19 23:21:33.056][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-03-19 23:21:33.060][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-03-19 23:21:33.061][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-03-19 23:21:33.063][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-03-19 23:21:33.065][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-03-19 23:21:33.067][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:21:33.068][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-03-19 23:21:33.070][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-03-19 23:21:33.072][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-03-19 23:21:33.074][biodb::testThat]
biodb.INFO [2025-03-19 23:21:33.075][biodb::testThat] Running test function  test.chebi.encoding.issue.in.xml  (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-03-19 23:21:33.077][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-03-19 23:21:33.078][biodb::testThat]
biodb.DEBUG[2025-03-19 23:21:33.082][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-03-19 23:21:33.087][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:33.089][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-03-19 23:21:33.091][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:33.094][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-03-19 23:21:33.100][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-03-19 23:21:33.106][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-03-19 23:21:33.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-03-19 23:21:33.111][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-03-19 23:21:33.115][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-03-19 23:21:33.122][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-03-19 23:21:33.123][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-03-19 23:21:33.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-03-19 23:21:33.127][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-03-19 23:21:33.129][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-03-19 23:21:33.131][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-03-19 23:21:33.133][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-03-19 23:21:33.134][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-03-19 23:21:33.136][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-03-19 23:21:33.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:33.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:33.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:33.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:33.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:33.153][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:33.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-03-19 23:21:33.156][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-03-19 23:21:33.160][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-03-19 23:21:33.162][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-03-19 23:21:33.164][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-03-19 23:21:33.511][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-03-19 23:21:34.142][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-03-19 23:21:34.145][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-03-19 23:21:34.151][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-03-19 23:21:34.156][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-03-19 23:21:34.161][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-03-19 23:21:34.164][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-03-19 23:21:34.166][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-03-19 23:21:34.169][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-03-19 23:21:34.171][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:34.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:34.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:34.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:34.382][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:34.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-03-19 23:21:34.392][ef$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.394][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.398][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.408][ef$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:34.410][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:34.412][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.414][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.416][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-03-19 23:21:34.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-03-19 23:21:34.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.424][ef$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:34.426][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:34.428][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.430][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.432][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-03-19 23:21:34.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-03-19 23:21:34.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.440][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-03-19 23:21:34.442][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-03-19 23:21:34.444][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.446][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.448][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-03-19 23:21:34.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-03-19 23:21:34.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.454][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.457][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:34.459][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:34.460][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.462][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.465][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:34.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-03-19 23:21:34.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.472][ef$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:34.474][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:34.476][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.478][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.481][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-03-19 23:21:34.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-03-19 23:21:34.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.489][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:34.491][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:34.492][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.494][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:34.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-03-19 23:21:34.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.505][ef$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:34.507][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:34.508][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.510][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.514][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-03-19 23:21:34.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-03-19 23:21:34.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.521][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:34.523][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:34.525][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.527][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.529][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-03-19 23:21:34.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-03-19 23:21:34.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.537][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:34.539][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:34.541][ef$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.543][ef$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.545][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-03-19 23:21:34.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-03-19 23:21:34.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:34.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:34.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:34.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:34.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.568][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-03-19 23:21:34.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-03-19 23:21:34.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.599][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-03-19 23:21:34.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-03-19 23:21:34.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-03-19 23:21:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-03-19 23:21:34.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-03-19 23:21:34.630][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-03-19 23:21:34.640][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-03-19 23:21:34.642][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-03-19 23:21:34.644][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-03-19 23:21:34.646][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-03-19 23:21:34.648][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-03-19 23:21:34.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-03-19 23:21:34.651][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-03-19 23:21:34.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-03-19 23:21:34.654][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-03-19 23:21:34.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
> 
> proc.time()
   user  system elapsed 
  28.54    2.17  119.61

Example timings

biodbChebi.Rcheck/biodbChebi-Ex.timings

name	user	system	elapsed
ChebiConn	4.34	2.52	207.06
ChebiEntry	0.61	0.03	1.33