Pierrick Roger
| Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_18 |
| git_last_commit: 664af9c |
| git_last_commit_date: 2023-10-24 11:36:37 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:32 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 196/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.8.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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. |
| Package: biodbChebi |
| Version: 1.8.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.8.0.tar.gz |
| StartedAt: 2024-04-15 23:54:29 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 23:58:34 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 245.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbChebi_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/biodbChebi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 4.555 1.123 66.52
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-04-15 23:56:58.907][biodb::testContext]
biodb.INFO [2024-04-15 23:56:58.915][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:56:58.917][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-04-15 23:56:58.920][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:56:58.922][biodb::testContext]
biodb.INFO [2024-04-15 23:56:58.937][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:56:58.941][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 23:56:58.956][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:56:58.958][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 23:56:58.961][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 23:56:58.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:58.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:58.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:58.971][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 23:56:59.022][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 23:56:59.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.032][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 23:56:59.035][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 23:56:59.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.044][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 23:56:59.047][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 23:56:59.050][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 23:56:59.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.144][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 23:56:59.147][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 23:56:59.150][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 23:56:59.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.160][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 23:56:59.163][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 23:56:59.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.173][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 23:56:59.175][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 23:56:59.178][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 23:56:59.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.188][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 23:56:59.190][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 23:56:59.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.201][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 23:56:59.204][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 23:56:59.207][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 23:56:59.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.219][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:56:59.221][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 23:56:59.223][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 23:56:59.226][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 23:56:59.229][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 23:56:59.232][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 23:56:59.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.239][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.DEBUG[2024-04-15 23:56:59.242][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 23:56:59.245][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 23:56:59.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.254][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 23:56:59.256][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 23:56:59.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.265][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 23:56:59.268][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 23:56:59.271][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.278][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 23:56:59.280][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 23:56:59.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.290][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 23:56:59.293][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 23:56:59.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.302][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:56:59.305][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 23:56:59.323][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 23:56:59.325][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.332][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 23:56:59.335][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 23:56:59.338][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 23:56:59.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.352][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 23:56:59.445][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.492][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 23:56:59.495][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.498][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:59.501][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.503][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.506][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.508][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.536][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:56:59.539][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:59.542][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.545][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 23:56:59.548][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:59.551][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.554][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.556][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:56:59.556][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:56:59.556][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:56:59.556][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:56:59.556][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:56:59.560][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:59.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.565][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.567][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:59.570][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.573][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.575][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.578][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.591][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:59.593][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:59.595][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.597][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.600][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 23:56:59.603][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.605][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:56:59.607][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.610][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:59.612][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.614][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.615][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.618][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.620][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:56:59.622][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:59.624][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.626][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 23:56:59.628][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:59.630][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.632][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.634][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:56:59.634][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:56:59.634][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:56:59.634][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:56:59.634][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:56:59.637][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:59.639][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.641][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.643][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:59.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.649][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.651][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.654][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:59.656][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:59.658][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.660][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.663][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 23:56:59.667][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.669][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 23:56:59.671][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.673][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:59.676][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.678][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.682][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.684][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:56:59.686][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:59.689][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.691][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 23:56:59.693][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:59.695][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.697][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.700][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.702][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:59.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.706][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:59.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.713][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.715][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.718][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.720][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:59.723][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:59.725][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.727][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.730][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 23:56:59.734][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.736][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:56:59.739][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.741][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:56:59.743][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.746][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.748][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.751][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.753][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:56:59.755][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:56:59.758][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.760][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 23:56:59.762][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:56:59.765][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.767][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:56:59.769][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.772][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:56:59.774][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.776][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.778][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:56:59.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:56:59.783][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:56:59.786][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:56:59.788][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.790][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:56:59.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:56:59.795][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:56:59.797][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:56:59.805][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:56:59.807][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.820][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[2024-04-15 23:56:59.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.828][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.859][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.861][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.870][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.878][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[2024-04-15 23:56:59.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.896][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[2024-04-15 23:56:59.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.907][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:56:59.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:56:59.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:56:59.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:56:59.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:56:59.996][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.DEBUG[2024-04-15 23:56:59.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.009][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 23:57:00.019][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 23:57:00.022][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 23:57:00.025][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 23:57:00.028][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:57:00.031][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 23:57:00.034][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 23:57:00.038][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 23:57:00.041][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 23:57:00.044][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 23:57:00.047][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:57:00.050][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 23:57:00.054][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 23:57:00.057][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 23:57:00.060][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 23:57:00.064][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:57:00.067][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 23:57:00.070][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 23:57:00.074][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:57:00.078][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 23:57:00.081][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 23:57:00.085][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 23:57:00.089][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 23:57:00.092][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 23:57:00.095][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 23:57:00.098][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 23:57:00.101][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 23:57:00.105][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 23:57:00.108][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 23:57:00.112][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 23:57:00.115][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 23:57:00.118][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 23:57:00.122][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 23:57:00.125][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 23:57:00.129][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 23:57:00.132][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 23:57:00.136][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 23:57:00.139][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 23:57:00.142][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 23:57:00.145][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 23:57:00.148][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 23:57:00.152][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 23:57:00.155][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 23:57:00.158][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 23:57:00.162][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 23:57:00.165][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 23:57:00.168][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 23:57:00.172][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 23:57:00.175][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 23:57:00.178][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 23:57:00.181][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 23:57:00.184][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 23:57:00.186][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 23:57:00.188][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 23:57:00.190][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 23:57:00.194][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 23:57:00.197][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 23:57:00.200][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 23:57:00.203][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 23:57:00.207][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 23:57:00.211][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 23:57:00.215][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 23:57:00.218][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 23:57:00.222][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 23:57:00.226][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 23:57:00.237][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 23:57:00.240][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:57:00.243][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:57:00.247][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 23:57:00.250][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 23:57:00.253][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 23:57:00.256][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 23:57:00.260][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 23:57:00.263][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 23:57:00.266][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 23:57:00.269][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 23:57:00.272][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 23:57:00.275][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 23:57:00.279][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 23:57:00.282][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 23:57:00.285][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 23:57:00.289][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 23:57:00.292][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 23:57:00.305][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 23:57:00.334][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:57:00.341][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:57:00.343][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.346][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.364][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.372][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.DEBUG[2024-04-15 23:57:00.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.382][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.394][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.407][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.431][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.453][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.459][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.496][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.526][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.546][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.550][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.558][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[2024-04-15 23:57:00.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:57:00.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:00.587][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-15 23:57:00.608][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-15 23:57:00.612][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:57:00.614][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 23:57:00.616][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:57:00.618][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:57:00.621][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:57:00.623][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:57:00.625][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 23:57:00.627][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-15 23:57:00.629][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-15 23:57:00.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:57:00.652][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:57:00.655][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-15 23:57:00.657][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-15 23:57:00.660][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-15 23:57:00.663][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 23:57:00.665][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:57:00.665][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:57:00.665][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:57:00.668][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-15 23:57:00.670][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:57:00.672][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:57:00.675][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:57:00.677][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:57:00.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:57:00.681][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:57:00.684][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:00.684][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-15 23:57:00.686][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:57:00.688][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:57:00.691][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 23:57:00.693][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-15 23:57:00.693][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-15 23:57:00.708][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:57:00.712][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:57:00.716][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-15 23:57:00.720][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:57:00.723][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:57:00.727][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:57:00.774][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-15 23:57:00.776][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-15 23:57:00.785][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-15 23:57:00.795][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-15 23:57:00.804][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:57:00.806][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:57:00.808][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-15 23:57:00.810][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-15 23:57:00.830][biodb::testThat]
biodb.INFO [2024-04-15 23:57:00.832][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-04-15 23:57:00.834][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:00.836][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:00.844][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-04-15 23:57:00.848][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:00.855][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:00.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:00.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:00.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:00.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:00.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:00.922][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:00.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:00.942][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:00.945][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:00.947][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:00.949][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:00.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:00.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:00.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:00.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:00.998][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:01.001][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:01.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.006][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.076][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:01.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:01.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.088][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:01.092][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:01.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.098][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:01.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:01.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.113][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:01.126][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:01.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.131][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:01.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:01.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.151][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.162][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.166][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.194][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:01.196][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:01.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.200][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.203][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:01.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:01.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.212][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:01.215][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:01.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.219][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.222][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:01.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:01.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.231][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:01.234][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:01.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.238][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:01.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:01.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.249][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:01.251][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:01.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.255][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:01.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:01.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.268][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:01.271][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:01.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.275][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.278][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:01.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:01.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.289][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:01.292][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:01.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.296][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.299][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:01.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:01.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.505][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:01.515][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-04-15 23:57:01.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:01.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:01.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:01.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:01.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.609][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.619][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:01.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:01.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:01.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:01.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:01.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:57:01.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:57:01.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.656][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:57:01.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:57:01.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.665][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 23:57:01.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 23:57:01.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.675][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 23:57:01.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 23:57:01.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.801][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:01.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.966][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.969][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.973][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:01.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:01.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:01.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:01.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.030][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.032][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.036][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:02.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.065][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:02.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:02.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.074][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:02.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:02.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:02.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:02.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.113][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:02.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:02.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.119][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:02.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:02.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:02.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:02.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.158][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:02.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:02.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.196][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:02.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:02.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.208][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:02.210][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:02.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.214][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.219][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:02.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:02.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.250][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.282][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.285][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.288][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.343][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.346][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.348][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.350][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.352][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.380][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:02.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:02.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.389][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:02.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:02.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.398][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:02.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:02.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.406][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:02.408][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:02.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.412][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.414][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:02.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:02.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.440][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.465][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.485][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.487][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.493][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.495][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:02.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.526][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.534][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.544][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.553][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.555][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.558][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.560][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.563][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.593][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:02.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:02.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:02.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:02.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.616][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:02.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:02.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.629][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:02.632][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:02.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.636][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.639][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:02.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:02.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.664][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.682][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.690][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.692][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.694][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.696][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.698][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.725][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:02.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:02.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:02.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:02.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.744][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:02.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:02.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.753][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:02.755][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:02.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.759][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.762][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:02.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:02.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.797][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:02.798][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:02.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.802][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.813][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:02.815][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:02.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.820][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.830][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:02.833][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:02.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.837][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.848][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:02.851][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:02.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.855][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.868][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.870][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:02.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.875][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.887][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.890][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:02.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.911][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.965][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.968][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:02.970][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.972][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.984][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:02.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:02.988][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:02.998][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-04-15 23:57:03.003][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:03.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:03.007][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:03.023][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:03.032][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:03.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:03.036][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:03.051][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:03.053][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:03.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:03.059][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:03.077][biodb::testThat]
biodb.INFO [2024-04-15 23:57:03.079][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-15 23:57:03.081][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:03.083][biodb::testThat]
biodb.DEBUG[2024-04-15 23:57:03.117][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-04-15 23:57:03.133][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:03.140][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.INFO [2024-04-15 23:57:03.142][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-04-15 23:57:03.145][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:03.148][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:03.150][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:03.153][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:03.155][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:03.157][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:03.167][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:03.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:03.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:03.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:03.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:03.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:03.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:03.190][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
biodb.DEBUG[2024-04-15 23:57:03.238][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:03.240][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:03.242][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440".
biodb.TRACE[2024-04-15 23:57:03.895][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15440).
biodb.DEBUG[2024-04-15 23:57:04.376][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:04.383][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.content"
biodb.TRACE[2024-04-15 23:57:04.420][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5c6fb88c946e8568cc03c0d73dc5603e.request"
biodb.TRACE[2024-04-15 23:57:04.428][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml"
biodb.DEBUG[2024-04-15 23:57:04.433][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:04.502][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:04.506][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:04.511][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:04.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:04.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:04.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:04.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:04.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:04.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:04.546][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:04.548][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:04.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.552][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:04.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:04.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.617][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:04.650][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:04.653][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.655][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.658][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:04.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:04.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.675][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:04.678][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:04.681][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.683][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:04.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:04.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.697][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:04.699][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:04.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.706][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:04.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.774][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:04.776][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:04.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.781][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.784][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:04.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:04.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.795][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:04.797][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:04.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.801][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.807][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:04.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:04.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.836][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:04.839][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:04.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.843][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.853][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:04.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:04.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.863][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:04.866][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:04.868][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.870][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:04.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:04.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.881][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:04.884][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:04.916][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.919][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.922][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:04.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.944][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:04.949][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:04.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.954][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.958][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:04.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.969][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:04.972][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:04.974][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.976][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.984][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:04.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:04.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:04.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:04.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:04.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:05.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:05.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:05.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:05.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:05.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:05.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:05.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:05.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:05.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:05.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:05.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:05.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:05.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:05.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:05.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:05.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:05.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:05.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:05.168][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-04-15 23:57:05.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-04-15 23:57:05.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-04-15 23:57:05.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-04-15 23:57:05.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-04-15 23:57:05.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-04-15 23:57:05.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-04-15 23:57:05.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:05.217][biodb::testThat]
biodb.INFO [2024-04-15 23:57:05.219][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-15 23:57:05.224][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:05.226][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:05.232][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:05.237][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:05.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.241][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:05.246][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-04-15 23:57:05.323][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:05.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:05.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:05.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:05.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:05.340][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:05.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:05.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:05.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:05.356][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-04-15 23:57:05.410][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-15 23:57:05.448][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:05.450][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:05.497][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-04-15 23:57:05.897][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-04-15 23:57:06.360][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:06.375][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-04-15 23:57:06.385][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-04-15 23:57:06.413][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:06.424][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:06.427][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:06.433][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:57:06.974][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:57:07.512][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:07.516][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-04-15 23:57:07.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-04-15 23:57:07.530][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-04-15 23:57:07.568][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:07.571][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:07.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:07.582][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:07.585][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:07.587][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:07.589][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:07.596][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:07.605][biodb::testThat]
biodb.INFO [2024-04-15 23:57:07.608][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-04-15 23:57:07.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:07.612][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:07.669][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:07.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:07.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:07.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:07.697][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:07.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:07.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:07.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:07.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:07.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:07.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:07.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:07.868][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:07.875][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:07.914][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-15 23:57:07.916][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:07.919][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-04-15 23:57:07.992][biodb::testThat]
biodb.INFO [2024-04-15 23:57:07.994][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-04-15 23:57:07.997][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:07.999][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:08.045][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:08.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:08.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:08.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:08.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.092][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.155][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.163][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.172][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 23:57:08.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 23:57:08.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.181][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 23:57:08.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 23:57:08.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.232][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:08.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:08.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:08.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:08.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:08.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.289][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.297][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 23:57:08.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.305][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 23:57:08.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 23:57:08.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:08.314][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 23:57:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 23:57:08.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:08.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:08.334][biodb::testThat]
biodb.INFO [2024-04-15 23:57:08.336][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-15 23:57:08.338][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:08.340][biodb::testThat]
biodb.INFO [2024-04-15 23:57:08.356][biodb::testThat]
biodb.INFO [2024-04-15 23:57:08.359][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-15 23:57:08.361][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:08.363][biodb::testThat]
biodb.INFO [2024-04-15 23:57:08.406][biodb::testThat]
biodb.INFO [2024-04-15 23:57:08.409][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-15 23:57:08.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:08.414][biodb::testThat]
biodb.DEBUG[2024-04-15 23:57:08.423][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-04-15 23:57:08.958][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-04-15 23:57:09.775][biodb::testThat]
biodb.INFO [2024-04-15 23:57:09.777][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-15 23:57:09.779][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:09.782][biodb::testThat]
biodb.DEBUG[2024-04-15 23:57:10.323][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-04-15 23:57:10.781][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:10.783][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:10.785][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:10.787][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:10.789][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:10.792][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:10.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:10.796][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:10.800][biodb::testThat]
biodb.INFO [2024-04-15 23:57:10.802][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-04-15 23:57:10.804][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:10.806][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:10.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:10.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:10.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:10.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:10.858][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:10.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:10.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:10.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:10.867][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:10.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:11.044][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:11.051][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:11.054][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-15 23:57:11.058][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:11.061][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-15 23:57:11.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:11.216][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:11.219][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-15 23:57:11.222][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:11.225][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-04-15 23:57:11.259][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 23:57:11.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 23:57:11.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:11.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:11.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:11.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:11.318][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:11.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:11.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:11.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:11.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:11.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:11.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:11.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:11.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:11.379][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:11.387][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:11.389][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:11.394][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:57:11.777][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:57:12.158][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:12.163][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-04-15 23:57:12.458][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-04-15 23:57:12.868][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:12.869][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:12.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:12.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:12.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:12.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:12.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:12.888][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-04-15 23:57:12.990][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:12.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-04-15 23:57:12.997][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:13.000][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:13.003][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:13.005][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:13.007][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:13.009][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:13.033][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:13.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:13.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:13.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:13.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:13.052][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:13.053][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[2024-04-15 23:57:13.055][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-04-15 23:57:13.062][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:13.068][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:13.071][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-04-15 23:57:13.454][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-04-15 23:57:13.837][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:13.841][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-04-15 23:57:13.914][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-04-15 23:57:13.920][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-04-15 23:57:13.925][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:13.928][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:13.931][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:13.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:13.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:13.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:13.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:13.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:13.958][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:13.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:13.964][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:13.967][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:13.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:13.971][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:13.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:13.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:13.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.001][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:14.003][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:14.005][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.007][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.009][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.016][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:14.018][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:14.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.021][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:14.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:14.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.033][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:14.036][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:14.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.059][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:14.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:14.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.070][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:14.094][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:14.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.099][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.102][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:14.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:14.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.112][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:14.114][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:14.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.119][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.121][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:14.124][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.128][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.131][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:14.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.139][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:14.142][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:14.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.146][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:14.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:14.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.160][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:14.164][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:14.166][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.168][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.170][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:14.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:14.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.176][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:14.177][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:14.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.181][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.182][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:14.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:14.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.191][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:14.193][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:14.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.197][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.199][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:14.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:14.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:14.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:14.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.216][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:14.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:14.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:14.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:14.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:14.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:14.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:14.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:14.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:14.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:14.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:14.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:14.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.345][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:14.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:14.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:14.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:14.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:14.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:14.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:14.432][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-04-15 23:57:14.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:14.474][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:14.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:14.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:14.532][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:14.541][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:14.543][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:14.545][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:57:14.929][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:57:15.316][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:15.330][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-04-15 23:57:15.359][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-04-15 23:57:15.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:15.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:15.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:15.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:15.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:15.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:15.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:15.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:15.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:15.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:15.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:15.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:15.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:15.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:15.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:15.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:15.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:15.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:15.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:15.457][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:15.459][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:15.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:15.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:15.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:15.475][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:15.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:15.480][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-04-15 23:57:15.482][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:15.486][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-04-15 23:57:15.488][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:15.490][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:15.492][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:15.495][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:15.497][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:15.499][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:15.505][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:15.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:15.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:15.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:15.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:15.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:15.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:15.525][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-04-15 23:57:15.529][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:15.531][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:15.534][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-04-15 23:57:15.911][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-04-15 23:57:16.289][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:16.292][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-04-15 23:57:16.312][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-04-15 23:57:16.379][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-04-15 23:57:16.422][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:16.425][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:16.427][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:16.431][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:16.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:16.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:16.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:16.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:16.448][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:16.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:16.454][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.456][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.460][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.463][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.471][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:16.474][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:16.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.478][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.480][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:16.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:16.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.489][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:16.491][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:16.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.494][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:16.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:16.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.504][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:16.506][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:16.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.510][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:16.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:16.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.521][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:16.523][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:16.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.527][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:16.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.536][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:16.538][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:16.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.542][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.545][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:16.547][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.548][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.549][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.551][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:16.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.558][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:16.561][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:16.563][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.565][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:16.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:16.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.574][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:16.576][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:16.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.581][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:16.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:16.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.592][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:16.594][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:16.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.598][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.601][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:16.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:16.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.611][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:16.613][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:16.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.616][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.618][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:16.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:16.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:16.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:16.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:16.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:16.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.648][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:16.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:16.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.658][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:16.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:16.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:16.699][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-04-15 23:57:16.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:16.755][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:16.760][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:16.762][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-15 23:57:16.764][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:16.766][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-15 23:57:16.769][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:16.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:16.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:16.783][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:16.785][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:16.787][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:16.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:16.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:16.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:16.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:16.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:16.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:16.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:16.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:16.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:16.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:16.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:16.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:16.883][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-04-15 23:57:16.886][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:16.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-04-15 23:57:16.892][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:16.895][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:16.897][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:16.900][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:16.902][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:16.905][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:16.910][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:16.912][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:16.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:16.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:16.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:16.929][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:16.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:16.934][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-04-15 23:57:16.941][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:16.943][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:16.951][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-04-15 23:57:17.326][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-04-15 23:57:17.702][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:17.706][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-04-15 23:57:17.714][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-04-15 23:57:17.884][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-04-15 23:57:18.130][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:18.133][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:18.136][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:18.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:18.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:18.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:18.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:18.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:18.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:18.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:18.163][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.165][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.170][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.182][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:18.185][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:18.187][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.190][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.193][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:18.195][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:18.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.199][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.202][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:18.205][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:18.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.209][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.212][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:18.214][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:18.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.219][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.223][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:18.225][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:18.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.230][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.233][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:18.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.276][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.279][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:18.281][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:18.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.285][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.287][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:18.289][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:18.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.293][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.296][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:18.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:18.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.318][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:18.320][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:18.322][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.324][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.326][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:18.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:18.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.332][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:18.334][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:18.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.338][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:18.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:18.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.345][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:18.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:18.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:18.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.366][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:18.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:18.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:18.415][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-04-15 23:57:18.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:18.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:18.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:18.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:18.462][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:18.464][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:18.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:18.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:18.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:18.480][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:18.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:18.484][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-04-15 23:57:18.486][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:18.490][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-04-15 23:57:18.493][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:18.495][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:18.498][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:18.500][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:18.502][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:18.504][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:18.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:18.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:18.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:18.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:18.526][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:18.528][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:18.529][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:18.532][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-04-15 23:57:18.538][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:18.539][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:18.543][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-04-15 23:57:18.919][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-04-15 23:57:19.302][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:19.306][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-04-15 23:57:19.314][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-04-15 23:57:19.343][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-04-15 23:57:19.347][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:19.350][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:19.353][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:19.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:19.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:19.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:19.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:19.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:19.375][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:19.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:19.381][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.384][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.387][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.398][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:19.400][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:19.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.404][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.407][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:19.410][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:19.412][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.415][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.418][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:19.421][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:19.423][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.425][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.427][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:19.429][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:19.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.434][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.437][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:19.439][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:19.441][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.443][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.446][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:19.449][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.454][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.457][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:19.460][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:19.462][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.464][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.467][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:19.469][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:19.471][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.503][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.507][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:19.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:19.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.517][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:19.534][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:19.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.538][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.541][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:19.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:19.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.552][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:19.554][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:19.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.559][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:19.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:19.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.572][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:19.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:19.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:19.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:19.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:19.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:19.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:19.654][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-04-15 23:57:19.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:19.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:19.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:19.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:19.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:19.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:19.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:19.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:19.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:19.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:19.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:19.743][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-04-15 23:57:19.745][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:19.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-04-15 23:57:19.751][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:19.752][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:19.754][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:19.756][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:19.758][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:19.759][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:19.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:19.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:19.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:19.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:19.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:19.784][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:19.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:19.789][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-04-15 23:57:19.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:19.797][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:19.800][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-04-15 23:57:20.182][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-04-15 23:57:20.574][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:20.578][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-04-15 23:57:20.616][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-04-15 23:57:20.622][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-04-15 23:57:20.625][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:20.628][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:20.631][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:20.634][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:20.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:20.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:20.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:20.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:20.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:20.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:20.660][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.663][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.668][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.682][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:20.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:20.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.689][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.692][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:20.694][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:20.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.698][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.701][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:20.703][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:20.705][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.707][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.710][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:20.712][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:20.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.716][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.719][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:20.721][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:20.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.726][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.728][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:20.731][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.735][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.738][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:20.741][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:20.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.746][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.748][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:20.751][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:20.753][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.755][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:20.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.769][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:20.771][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:20.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.790][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.793][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:20.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:20.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.801][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:20.804][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:20.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.808][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:20.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:20.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:20.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:20.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.837][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:20.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:20.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:20.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:20.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:20.899][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-04-15 23:57:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:20.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:20.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:20.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:20.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:20.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:20.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:20.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:20.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:20.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:20.957][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-04-15 23:57:20.959][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:20.963][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-04-15 23:57:20.966][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:20.968][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:20.971][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:20.974][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:20.976][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:20.978][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:20.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:20.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:20.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:20.995][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:20.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:20.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:21.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:21.004][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-04-15 23:57:21.009][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:21.012][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:21.026][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-04-15 23:57:21.404][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-04-15 23:57:21.784][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:21.788][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-04-15 23:57:21.797][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-04-15 23:57:21.883][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-04-15 23:57:21.887][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:21.890][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:21.892][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:21.895][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:21.897][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:21.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:21.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:21.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:21.916][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:21.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:21.924][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:21.927][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:21.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:21.932][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:21.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:21.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:21.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:21.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:21.953][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:21.956][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:21.958][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:21.962][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:21.965][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:21.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:21.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:21.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:21.975][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:21.978][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:21.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:21.982][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:21.986][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:21.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:21.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:21.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:21.995][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:21.998][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:22.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.002][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:22.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:22.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.015][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:22.017][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:22.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.023][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.025][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:22.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:22.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.035][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:22.038][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:22.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.043][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.045][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:22.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:22.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.055][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:22.071][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.089][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.092][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:22.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.102][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:22.104][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:22.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.108][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:22.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:22.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.121][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:22.124][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:22.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.128][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:22.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:22.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.143][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:22.145][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:22.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.149][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.151][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:22.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:22.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.160][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:22.163][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:22.165][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.167][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.170][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:22.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:22.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:22.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:22.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:22.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:22.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.208][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:22.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:22.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:22.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:22.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:22.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:22.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:22.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:22.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:22.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:22.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:22.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:22.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:22.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:22.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:22.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:22.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:22.281][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-04-15 23:57:22.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:22.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:22.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:22.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:22.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:22.309][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:22.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:22.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:22.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:22.323][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:22.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:22.328][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-04-15 23:57:22.330][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:22.349][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-04-15 23:57:22.352][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:22.354][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:22.357][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:22.360][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:22.362][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:22.365][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:22.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:22.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:22.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:22.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:22.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:22.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:22.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:22.414][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-04-15 23:57:22.419][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:22.422][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:22.424][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-04-15 23:57:22.809][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-04-15 23:57:23.205][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:23.209][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-04-15 23:57:23.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-04-15 23:57:23.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-04-15 23:57:23.263][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:23.266][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:23.269][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:23.272][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:23.274][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:23.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:23.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:23.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:23.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:23.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:23.300][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.303][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.307][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.322][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:23.324][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:23.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.329][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.332][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:23.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:23.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.341][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:23.360][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:23.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.365][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.368][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:23.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:23.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.377][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:23.379][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:23.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.383][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:23.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:23.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.408][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:23.411][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:23.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.415][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:23.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:23.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.430][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:23.432][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:23.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.439][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.442][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:23.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:23.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.451][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:23.454][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.460][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.463][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:23.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.477][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:23.480][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:23.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.489][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.492][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:23.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:23.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.504][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:23.506][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:23.508][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.510][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.513][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:23.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:23.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.523][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:23.525][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:23.528][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.530][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.533][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:23.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:23.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.542][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:23.544][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:23.547][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.549][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.551][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:23.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:23.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:23.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:23.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:23.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:23.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:23.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:23.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:23.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:23.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:23.671][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-04-15 23:57:23.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.682][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:23.692][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:23.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:23.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:23.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:23.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:23.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:23.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:23.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:23.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:23.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:23.725][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-04-15 23:57:23.747][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:23.751][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-04-15 23:57:23.754][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:23.757][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:23.761][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:23.763][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:23.766][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:23.769][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:23.775][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:23.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:23.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:23.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:23.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:23.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:23.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:23.800][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-04-15 23:57:23.807][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:23.810][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:23.814][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-04-15 23:57:24.211][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-04-15 23:57:24.609][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:24.613][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-04-15 23:57:24.648][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-04-15 23:57:24.655][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-04-15 23:57:24.659][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:24.662][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:24.665][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:24.668][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:24.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:24.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:24.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:24.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:24.686][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:24.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:24.693][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:24.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:24.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.699][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:24.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:24.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.724][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:24.729][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:24.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.733][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.736][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:24.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:24.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.744][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:24.747][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:24.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.751][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:24.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:24.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.762][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:24.765][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:24.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.769][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.772][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:24.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:24.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.781][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:24.796][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:24.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.800][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:24.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:24.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.813][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:24.815][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:24.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.820][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.823][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:24.825][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:24.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.829][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.832][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:24.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:24.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.842][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:24.844][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:24.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.848][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:24.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:24.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.862][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:24.864][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:24.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.869][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.872][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:24.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.882][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:24.885][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:24.887][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.889][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.892][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:24.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.899][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.901][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:24.904][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:24.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.908][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.911][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:24.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:24.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.924][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:24.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:24.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:24.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:24.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:24.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:24.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:24.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:24.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:24.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:24.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:24.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:24.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:24.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:24.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:24.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:25.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:25.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:25.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:25.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:25.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:25.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:25.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:25.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:25.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:25.022][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-04-15 23:57:25.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:25.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:25.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:25.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:25.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:25.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:25.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:25.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:25.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:25.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:25.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:25.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:25.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:25.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:25.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:25.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:25.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:25.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:25.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:25.097][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-04-15 23:57:25.100][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:25.103][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-04-15 23:57:25.106][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:25.127][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:25.130][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:25.132][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:25.135][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:25.137][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:25.143][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:25.146][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:25.148][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:25.178][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:25.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:25.183][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:25.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:25.188][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-04-15 23:57:25.194][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:25.196][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:25.199][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-04-15 23:57:25.580][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-04-15 23:57:25.961][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:25.965][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-04-15 23:57:25.974][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-04-15 23:57:25.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-04-15 23:57:25.985][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:25.988][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:25.998][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:26.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:26.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:26.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:26.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:26.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:26.042][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:26.044][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[2024-04-15 23:57:26.051][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.053][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.058][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.069][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:26.072][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:26.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.076][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:26.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:26.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.088][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:26.090][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:26.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.095][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.112][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:26.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:26.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.121][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:26.124][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:26.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.128][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:26.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:26.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.140][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:26.142][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:26.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.146][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:26.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:26.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.162][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:26.164][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:26.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.169][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.171][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:26.174][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.176][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.178][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.180][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:26.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.189][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:26.193][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:26.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.197][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:26.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:26.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.208][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.212][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:26.215][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:26.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.220][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.224][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:26.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:26.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.232][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:26.235][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:26.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.239][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.242][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:26.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:26.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.251][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:26.254][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:26.256][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.258][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.261][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:26.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:26.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:26.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:26.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:26.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:26.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:26.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:26.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.316][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:26.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:26.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:26.363][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-04-15 23:57:26.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:26.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:26.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:26.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:26.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:26.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:26.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:26.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:26.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:26.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:26.417][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:26.419][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-04-15 23:57:26.421][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:26.425][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-04-15 23:57:26.428][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:26.430][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:26.433][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:26.435][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:26.437][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:26.457][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:26.465][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:26.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:26.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:26.482][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:26.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:26.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:26.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:26.500][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-04-15 23:57:26.508][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:26.510][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:26.513][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-04-15 23:57:26.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-04-15 23:57:27.283][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:27.288][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-04-15 23:57:27.296][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-04-15 23:57:27.302][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-04-15 23:57:27.306][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:27.309][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:27.322][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:27.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:27.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:27.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:27.358][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:27.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:27.362][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:27.364][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[2024-04-15 23:57:27.369][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.371][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.376][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.387][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:27.389][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:27.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.393][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.396][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:27.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:27.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.408][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:27.411][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:27.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.423][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.425][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:27.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:27.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.437][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:27.440][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:27.442][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.444][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.447][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:27.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:27.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.455][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:27.458][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:27.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.462][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:27.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:27.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.475][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:27.477][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:27.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.481][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.484][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:27.486][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.488][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.490][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.493][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:27.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:27.503][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:27.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.526][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.529][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:27.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:27.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.538][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:27.541][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:27.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.546][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:27.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:27.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.559][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:27.562][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:27.564][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.566][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:27.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:27.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.578][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:27.580][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:27.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.584][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.590][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:27.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:27.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:27.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:27.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:27.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:27.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:27.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:27.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.670][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:27.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:27.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:27.707][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-04-15 23:57:27.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:27.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:27.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:27.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:27.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:27.738][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:27.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:27.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:27.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:27.756][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:27.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:27.760][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-04-15 23:57:27.762][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:27.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-04-15 23:57:27.783][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:27.786][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:27.793][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:27.795][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:27.799][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:27.801][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:27.807][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:27.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:27.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:27.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:27.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:27.824][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:27.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:27.829][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-04-15 23:57:27.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:27.836][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:27.839][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-04-15 23:57:28.217][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-04-15 23:57:28.598][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:28.603][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-04-15 23:57:28.619][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-04-15 23:57:28.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-04-15 23:57:28.630][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:28.633][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:28.635][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:28.639][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:28.641][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:28.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:28.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:28.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:28.661][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:28.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:28.672][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.674][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.680][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.692][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:28.694][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:28.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.699][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.701][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:28.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.710][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:28.712][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:28.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.717][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.719][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:28.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:28.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.728][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:28.731][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:28.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.735][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.738][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:28.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:28.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.748][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:28.750][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:28.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.755][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:28.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:28.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.767][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:28.769][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:28.771][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.773][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.776][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:28.779][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:28.781][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.798][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.801][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:28.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:28.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.812][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:28.815][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:28.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.819][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:28.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:28.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.833][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:28.836][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:28.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.840][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:28.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.853][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:28.856][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:28.858][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.860][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.863][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:28.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:28.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.872][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:28.875][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:28.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.879][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.882][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:28.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:28.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:28.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:28.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:28.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:28.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:28.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:28.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:28.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:28.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:28.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:28.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:29.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:29.003][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-04-15 23:57:29.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:29.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:29.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:29.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:29.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:29.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:29.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:29.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:29.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:29.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:29.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:29.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:29.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:29.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:29.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:29.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:29.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:29.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:29.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:29.070][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-04-15 23:57:29.072][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:29.076][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-04-15 23:57:29.079][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:29.081][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:29.084][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:29.086][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:29.089][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:29.091][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:29.097][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:29.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:29.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:29.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:29.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:29.120][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:29.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:29.125][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-04-15 23:57:29.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:29.134][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:29.137][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-04-15 23:57:31.169][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-04-15 23:57:31.551][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:31.556][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-04-15 23:57:31.564][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-04-15 23:57:31.571][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-04-15 23:57:31.576][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:31.580][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:31.595][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:31.599][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:31.602][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:31.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:31.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:31.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:31.628][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:31.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:31.634][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:31.636][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:31.639][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.641][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:31.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:31.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.652][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:31.655][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:31.656][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.658][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.660][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:31.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:31.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.688][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:31.690][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:31.693][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.694][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.697][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:31.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:31.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.706][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:31.708][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:31.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.712][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:31.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:31.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.721][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:31.723][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:31.725][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.727][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:31.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:31.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.738][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:31.741][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:31.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.745][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.748][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:31.752][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:31.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.756][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.767][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:31.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:31.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.778][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:31.780][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:31.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.785][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:31.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:31.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.798][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:31.800][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:31.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.804][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:31.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:31.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.816][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:31.818][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:31.820][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.822][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.825][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:31.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:31.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.835][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:31.837][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:31.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.841][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.844][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:31.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:31.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:31.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:31.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:31.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:31.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:31.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:31.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:31.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:31.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:31.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:31.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:31.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:31.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:31.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:31.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:31.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:31.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:32.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:32.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:32.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:32.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:32.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:32.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:32.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:32.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:32.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:32.027][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-04-15 23:57:32.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:32.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:32.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:32.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:32.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:32.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:32.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:32.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:32.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:32.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:32.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:32.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:32.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:32.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:32.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:32.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:32.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:32.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:32.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:32.081][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-04-15 23:57:32.083][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:32.086][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-04-15 23:57:32.089][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:32.092][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:32.095][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:32.097][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:32.099][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:32.132][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:32.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:32.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:32.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:32.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:32.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:32.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:32.193][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:32.195][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-04-15 23:57:32.202][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:32.204][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:32.207][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-04-15 23:57:32.591][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-04-15 23:57:32.969][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:32.972][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-04-15 23:57:32.980][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-04-15 23:57:32.986][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-04-15 23:57:32.989][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:32.992][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:32.995][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:32.998][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:33.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:33.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:33.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:33.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:33.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:33.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:33.023][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.043][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.055][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:33.058][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:33.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.062][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.065][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:33.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:33.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.074][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:33.076][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:33.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.080][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.083][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:33.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:33.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.092][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:33.094][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:33.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.099][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.102][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:33.104][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:33.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.108][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.111][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:33.113][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:33.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.118][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.121][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:33.123][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.127][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.129][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:33.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.138][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:33.141][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:33.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.146][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:33.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:33.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.159][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:33.161][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:33.163][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.165][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.168][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:33.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:33.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.177][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:33.179][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:33.181][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.184][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:33.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:33.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.198][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:33.201][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:33.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.206][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:33.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:33.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:33.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:33.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:33.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:33.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:33.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:33.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:33.336][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-04-15 23:57:33.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:33.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:33.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:33.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:33.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:33.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:33.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:33.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:33.388][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:33.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:33.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:33.395][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-04-15 23:57:33.397][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:33.401][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-04-15 23:57:33.418][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:33.421][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:33.424][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:33.427][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:33.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:33.432][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:33.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:33.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:33.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:33.467][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:33.469][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:33.471][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:33.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:33.476][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-04-15 23:57:33.483][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:33.485][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:33.489][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-04-15 23:57:33.869][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-04-15 23:57:34.258][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:34.263][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-04-15 23:57:34.271][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-04-15 23:57:34.278][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-04-15 23:57:34.284][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:34.287][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:34.290][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:34.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:34.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:34.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:34.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:34.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:34.315][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:34.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:34.322][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.325][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.329][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.363][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:34.366][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:34.367][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.369][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.371][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:34.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:34.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.378][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:34.380][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:34.381][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.382][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.383][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:34.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:34.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.388][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:34.390][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:34.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.392][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.394][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:34.395][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:34.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.397][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.400][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:34.402][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:34.405][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.407][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.410][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:34.413][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.417][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.419][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:34.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.428][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:34.431][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:34.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.436][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.439][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:34.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:34.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.453][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:34.456][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:34.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.463][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.467][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:34.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:34.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.496][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:34.499][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:34.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.503][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.506][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:34.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:34.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.515][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:34.517][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:34.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.521][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:34.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:34.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.533][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:34.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:34.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.542][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:34.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:34.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.559][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.593][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.603][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:34.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:34.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:34.630][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-04-15 23:57:34.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:34.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:34.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:34.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:34.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:34.659][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:34.661][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:34.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:34.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:34.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:34.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:34.680][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-04-15 23:57:34.683][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:34.686][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-04-15 23:57:34.689][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:34.692][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:34.715][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:34.718][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:34.721][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:34.723][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:34.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:34.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:34.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:34.774][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:34.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:34.778][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:34.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:34.782][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-04-15 23:57:34.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:34.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:34.794][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-04-15 23:57:35.204][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-04-15 23:57:35.589][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:35.593][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-04-15 23:57:35.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-04-15 23:57:35.606][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-04-15 23:57:35.610][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:35.613][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:35.615][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:35.619][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:35.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:35.623][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:35.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:35.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:35.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:35.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:35.663][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.665][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.671][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.684][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:35.686][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:35.688][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.691][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.694][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:35.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:35.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.704][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:35.706][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:35.708][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.710][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:35.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:35.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.724][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:35.727][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:35.729][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.731][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.734][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:35.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:35.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.746][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:35.748][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:35.750][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.753][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:35.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:35.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.768][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:35.771][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:35.773][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.778][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.781][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:35.783][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:35.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.790][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.792][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:35.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:35.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:35.806][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:35.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.810][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:35.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:35.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.824][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:35.827][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:35.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.832][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.836][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:35.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:35.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.845][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:35.848][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:35.850][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.852][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.855][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:35.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:35.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.865][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:35.868][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:35.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.872][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.875][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:35.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:35.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:35.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:35.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.909][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:35.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:35.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:35.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:35.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:35.992][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:35.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:35.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:35.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:36.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:36.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:36.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:36.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:36.010][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-04-15 23:57:36.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:36.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:36.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:36.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:36.021][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:36.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:36.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:36.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:36.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:36.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:36.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:36.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:36.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:36.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:36.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:36.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:36.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:36.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:36.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:36.064][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-04-15 23:57:36.066][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:36.070][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-04-15 23:57:36.073][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:36.076][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:36.079][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:36.081][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:36.084][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:36.086][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:36.093][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:36.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:36.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:36.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:36.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:36.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:36.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:36.120][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-04-15 23:57:36.126][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:36.129][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:36.132][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-04-15 23:57:36.512][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-04-15 23:57:36.890][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:36.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-04-15 23:57:36.919][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-04-15 23:57:36.926][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-04-15 23:57:36.930][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:36.933][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:36.936][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:36.940][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:36.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:36.944][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:36.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:36.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:36.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:36.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:36.970][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:36.973][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:36.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:36.979][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:36.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:36.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:36.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:36.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:36.992][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:36.995][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:36.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.000][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.004][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:37.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:37.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.015][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:37.017][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:37.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.022][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.025][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:37.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:37.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.035][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:37.038][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:37.043][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.046][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:37.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:37.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.062][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:37.064][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:37.066][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.070][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.073][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:37.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.082][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:37.085][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:37.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.089][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.092][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:37.094][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.099][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.101][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:37.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.112][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:37.114][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:37.116][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.119][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:37.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:37.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.132][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:37.135][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:37.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.139][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.143][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:37.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:37.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.167][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:37.170][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:37.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.174][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.177][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:37.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:37.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.187][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:37.189][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:37.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.194][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.213][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:37.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:37.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:37.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:37.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.234][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:37.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:37.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:37.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:37.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:37.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:37.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:37.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:37.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.278][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:37.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:37.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:37.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:37.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.298][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:37.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:37.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:37.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:37.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:37.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:37.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:37.328][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-04-15 23:57:37.331][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.340][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:37.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:37.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:37.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:37.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:37.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:37.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:37.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:37.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:37.388][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:37.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:37.392][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-04-15 23:57:37.394][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:37.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-04-15 23:57:37.402][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:37.404][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:37.407][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:37.410][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:37.412][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:37.415][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:37.421][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:37.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:37.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:37.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:37.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:37.440][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:37.442][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:37.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-04-15 23:57:37.450][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:37.452][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:37.455][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-04-15 23:57:37.834][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-04-15 23:57:38.224][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:38.228][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-04-15 23:57:38.239][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-04-15 23:57:38.245][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-04-15 23:57:38.249][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:38.252][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:38.255][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:38.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:38.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:38.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:38.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:38.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:38.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:38.283][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[2024-04-15 23:57:38.289][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.292][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.296][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.309][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:38.312][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:38.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.316][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.319][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:38.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:38.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.387][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:38.389][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:38.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.394][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.396][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:38.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:38.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.405][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:38.407][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:38.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.412][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.415][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:38.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:38.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.425][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:38.428][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:38.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.432][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:38.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:38.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.447][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:38.450][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:38.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.460][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.463][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:38.466][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.473][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.476][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:38.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.501][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:38.504][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:38.506][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.508][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:38.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:38.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.521][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:38.524][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:38.527][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.529][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:38.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:38.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.544][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:38.547][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:38.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.591][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.594][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:38.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:38.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.603][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:38.605][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:38.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.609][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.612][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:38.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:38.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.683][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:38.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:38.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:38.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:38.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:38.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:38.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:38.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:38.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:38.910][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-04-15 23:57:38.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:38.940][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:38.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:38.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:38.954][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:38.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:38.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:38.969][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:38.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:38.974][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:38.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:38.979][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-04-15 23:57:38.981][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:38.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-04-15 23:57:38.988][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:38.991][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:38.994][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:38.996][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:38.999][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:39.001][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:39.007][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:39.009][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:39.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:39.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:39.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:39.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:39.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:39.031][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-04-15 23:57:39.038][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:39.040][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:39.043][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-04-15 23:57:39.422][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-04-15 23:57:39.802][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:39.806][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-04-15 23:57:39.815][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-04-15 23:57:39.821][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-04-15 23:57:39.825][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:39.828][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:39.830][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:39.834][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:39.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:39.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:39.868][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:39.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:39.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:39.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:39.921][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:39.923][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:39.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:39.928][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:39.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:39.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:39.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:39.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:39.941][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:39.943][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:39.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:39.946][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:39.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:39.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:39.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:39.959][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:39.961][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:39.964][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:39.966][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:39.969][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:39.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:39.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:39.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:39.990][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:39.992][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:39.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:39.999][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:40.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:40.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.011][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:40.027][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:40.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.032][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:40.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:40.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.044][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:40.047][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:40.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.051][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.054][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:40.056][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.060][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.063][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:40.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.085][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:40.088][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:40.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.093][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:40.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:40.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.107][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:40.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:40.112][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.115][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:40.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:40.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.129][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:40.131][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:40.134][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.136][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.140][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:40.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:40.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.149][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:40.152][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:40.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.156][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.159][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:40.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:40.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:40.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:40.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:40.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:40.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:40.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:40.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:40.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:40.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:40.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:40.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:40.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:40.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:40.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:40.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:40.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:40.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:40.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:40.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:40.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:40.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:40.270][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-04-15 23:57:40.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:40.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:40.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:40.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:40.292][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:40.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:40.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:40.308][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:40.310][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:40.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:40.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:40.318][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-04-15 23:57:40.321][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:40.325][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-04-15 23:57:40.328][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:40.330][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:40.333][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:40.335][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:40.338][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:40.340][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:40.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:40.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:40.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:40.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:40.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:40.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:40.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:40.400][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-04-15 23:57:40.407][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:40.409][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:40.413][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-04-15 23:57:40.795][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-04-15 23:57:41.174][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:41.179][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-04-15 23:57:41.188][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-04-15 23:57:41.195][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-04-15 23:57:41.199][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:41.202][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:41.204][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:41.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:41.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:41.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:41.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:41.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:41.226][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:41.228][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.TRACE[2024-04-15 23:57:41.233][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.236][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.238][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.240][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.252][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:41.255][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:41.257][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.259][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.261][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:41.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:41.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.285][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:41.287][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:41.289][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.291][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.294][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:41.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:41.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.335][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:41.338][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:41.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.344][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:41.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:41.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.357][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:41.360][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:41.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.365][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.368][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:41.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:41.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.377][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:41.380][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:41.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.385][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.388][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:41.390][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.394][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.397][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:41.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.405][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:41.408][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:41.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.412][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:41.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:41.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.423][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:41.425][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:41.427][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.429][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.432][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:41.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:41.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.441][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:41.445][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:41.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.449][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.452][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:41.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.464][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:41.467][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:41.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.471][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.474][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:41.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:41.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:41.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:41.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:41.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:41.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:41.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:41.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.571][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.579][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:41.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:41.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:41.588][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-04-15 23:57:41.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:41.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:41.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:41.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:41.616][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:41.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:41.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:41.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:41.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:41.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:41.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:41.647][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-04-15 23:57:41.650][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:41.654][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-04-15 23:57:41.657][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:41.660][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:41.662][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:41.664][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:41.667][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:41.669][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:41.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:41.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:41.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:41.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:41.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:41.692][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:41.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:41.713][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-04-15 23:57:41.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:41.763][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:41.768][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-04-15 23:57:42.145][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-04-15 23:57:42.529][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:42.541][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-04-15 23:57:42.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-04-15 23:57:42.555][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-04-15 23:57:42.559][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:42.562][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:42.565][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:42.569][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:42.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:42.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:42.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:42.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:42.605][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:42.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:42.613][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.615][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.620][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.622][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.632][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:42.635][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:42.637][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.640][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.643][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:42.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:42.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.654][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:42.657][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:42.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.662][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.665][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:42.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:42.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.679][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:42.683][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:42.686][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.688][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.690][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:42.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:42.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.699][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:42.702][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:42.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.706][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.709][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:42.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:42.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.719][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:42.731][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:42.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.735][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.738][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:42.740][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.746][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.749][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:42.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.759][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:42.761][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:42.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.766][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:42.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:42.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.779][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:42.781][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:42.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.786][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.789][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:42.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:42.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.798][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:42.801][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:42.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.806][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.809][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:42.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:42.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.818][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:42.820][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:42.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.825][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.828][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:42.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:42.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:42.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:42.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:42.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:42.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:42.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:42.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:42.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:42.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:42.926][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-04-15 23:57:42.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:42.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:42.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:42.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:42.959][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:42.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:42.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:42.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:42.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:42.980][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:42.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:42.985][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-04-15 23:57:42.987][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:42.991][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-04-15 23:57:42.994][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:42.997][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:43.000][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:43.025][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:43.027][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:43.030][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:43.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:43.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:43.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:43.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:43.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:43.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:43.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:43.096][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-04-15 23:57:43.102][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:43.104][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:43.107][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-04-15 23:57:43.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-04-15 23:57:43.874][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:43.891][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-04-15 23:57:43.898][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-04-15 23:57:43.904][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-04-15 23:57:43.907][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:43.910][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:43.912][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:43.916][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:43.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:43.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:43.930][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:43.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:43.934][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:43.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:43.940][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:43.942][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:43.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:43.947][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:43.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:43.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:43.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:43.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:43.972][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:43.974][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:43.976][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:43.977][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:43.980][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:43.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:43.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:43.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:43.988][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:43.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:43.991][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:43.992][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:43.995][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:43.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:43.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.002][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:44.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:44.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.008][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:44.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:44.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.021][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:44.023][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:44.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.026][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.029][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:44.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:44.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.037][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:44.040][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:44.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.045][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.047][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:44.053][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.058][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.064][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:44.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.073][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:44.079][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:44.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.084][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:44.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:44.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.097][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:44.099][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:44.101][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.104][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:44.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:44.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.116][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:44.118][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:44.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.122][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.124][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:44.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:44.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.133][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:44.135][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:44.137][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.139][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.142][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:44.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:44.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:44.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:44.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:44.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:44.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:44.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:44.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:44.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:44.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:44.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:44.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:44.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:44.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:44.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:44.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:44.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:44.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:44.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:44.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:44.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:44.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.255][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-04-15 23:57:44.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.325][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:44.332][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:44.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-15 23:57:44.357][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:44.360][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-15 23:57:44.365][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.367][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.395][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.403][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.412][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.414][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.430][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.441][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.495][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.594][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.659][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.686][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.714][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.732][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.740][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.762][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.796][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.830][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.864][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.866][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.868][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.896][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:44.932][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:44.934][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:44.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:44.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:44.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:44.981][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:44.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:44.985][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:44.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:44.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:44.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.028][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.040][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.111][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.134][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.186][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.235][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.253][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.273][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.397][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.413][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.417][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.440][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.449][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.462][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.487][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.498][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.520][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.578][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:45.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:45.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:45.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:45.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:45.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:45.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:45.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:45.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:45.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:45.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:45.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:45.791][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:45.798][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:45.800][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:45.806][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:57:46.189][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:57:46.572][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:46.634][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-04-15 23:57:46.643][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-04-15 23:57:46.666][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:46.674][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:46.677][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:46.681][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:57:47.079][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:57:47.466][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:47.470][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-04-15 23:57:47.479][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-04-15 23:57:47.485][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:47.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:47.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:47.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:47.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:47.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:47.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:47.508][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-04-15 23:57:47.510][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:47.525][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-04-15 23:57:47.528][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:47.531][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:47.533][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:47.535][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:47.537][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:47.539][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:47.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:47.547][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:47.548][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:47.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:47.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:47.578][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:47.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:47.582][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-04-15 23:57:47.588][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:47.590][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:47.593][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-04-15 23:57:47.978][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-04-15 23:57:48.364][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:48.368][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-04-15 23:57:48.374][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-04-15 23:57:48.380][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-04-15 23:57:48.384][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:48.386][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:48.389][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:48.392][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:48.394][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:48.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:48.406][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:48.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:48.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:48.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:48.416][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.419][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.421][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.422][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.425][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.433][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:48.447][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:48.449][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.452][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.455][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:48.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:48.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.462][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:48.465][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:48.466][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.468][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:48.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:48.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.482][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:48.484][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:48.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.487][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.490][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:48.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:48.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.499][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:48.502][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:48.504][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.505][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:48.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:48.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.516][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:48.518][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:48.521][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.523][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.525][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:48.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:48.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.534][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:48.537][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:48.539][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.541][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.543][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:48.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:48.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.552][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.555][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.559][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.574][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:48.576][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:48.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.581][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:48.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:48.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.593][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:48.595][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:48.597][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.599][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.602][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:48.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:48.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.610][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:48.612][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:48.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.617][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.619][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:48.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:48.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:48.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:48.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:48.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:48.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:48.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:48.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:48.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:48.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:48.748][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-04-15 23:57:48.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:48.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:48.786][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:48.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:48.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:48.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:48.802][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:48.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:48.807][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:48.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:48.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:48.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:48.841][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:48.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:48.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:48.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:48.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:48.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:48.878][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:48.880][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-04-15 23:57:48.882][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:57:48.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-04-15 23:57:48.888][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:57:48.890][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:57:48.893][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:57:48.895][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:57:48.897][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:57:48.900][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:57:48.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:48.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:48.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:48.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:48.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:48.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:48.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:48.928][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-04-15 23:57:48.934][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:48.936][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:48.939][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-04-15 23:57:49.321][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-04-15 23:57:49.706][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:49.710][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-04-15 23:57:49.721][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-04-15 23:57:49.727][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-04-15 23:57:49.730][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:57:49.733][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:57:49.736][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:57:49.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:49.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:49.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:49.755][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:49.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:49.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:49.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:49.767][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:49.772][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:49.774][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.776][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:49.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:49.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.789][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:49.791][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:49.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.795][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.798][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:57:49.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:57:49.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.807][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:49.810][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:49.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.814][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.828][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:57:49.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:57:49.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.839][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:49.842][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:49.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.847][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:57:49.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:57:49.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.856][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.858][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:49.861][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:49.863][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.865][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:57:49.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:57:49.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.877][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:49.879][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:57:49.882][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.884][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.887][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:49.889][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:49.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.893][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.896][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:57:49.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:49.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.906][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:49.922][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:49.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.927][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:49.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:49.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.940][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:49.943][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:49.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.951][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:57:49.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:57:49.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.965][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:49.967][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:49.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.971][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.974][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:57:49.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:57:49.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.983][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:49.986][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:49.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:49.990][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:49.993][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:57:49.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:57:49.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:50.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:50.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:50.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:50.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:50.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:50.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:50.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:50.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:50.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:50.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:50.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:50.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:50.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:50.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:57:50.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:57:50.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.103][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-04-15 23:57:50.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.125][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.186][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:50.194][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:50.197][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-15 23:57:50.200][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:50.203][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-15 23:57:50.211][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.318][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.336][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.377][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.497][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.545][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.587][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.596][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.623][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.649][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.708][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.711][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.727][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.733][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.785][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.885][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.892][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.910][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:50.950][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:50.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:50.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:50.964][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:50.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:50.968][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:50.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:50.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:50.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:50.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.008][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.047][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.054][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.077][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.093][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.141][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.143][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.174][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.207][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.224][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.302][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.352][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.385][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.404][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.512][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.535][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.590][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:51.605][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:51.608][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-04-15 23:57:51.611][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:51.614][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-04-15 23:57:51.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.623][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.637][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.674][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.720][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.759][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.766][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.778][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.832][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.834][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.852][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.896][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.917][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.933][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:51.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:51.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:51.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:51.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:51.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:51.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:51.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:51.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:51.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:51.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:51.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.023][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.039][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.075][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.083][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.190][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.252][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.276][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.351][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.384][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.434][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.438][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.449][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.455][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.517][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.530][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.604][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.621][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.627][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.655][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.673][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.687][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.722][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.763][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.773][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.823][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:52.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:52.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:52.829][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:52.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:52.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:52.847][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:52.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:52.851][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:52.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:52.967][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 23:57:52.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 23:57:52.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:52.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:52.994][biodb::testThat]
biodb.INFO [2024-04-15 23:57:52.995][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-04-15 23:57:52.998][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:52.999][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:53.017][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 23:57:53.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 23:57:53.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.050][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:53.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:53.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:53.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:53.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:53.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:53.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:53.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:53.113][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:53.121][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:53.124][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-04-15 23:57:53.126][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:53.129][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-04-15 23:57:53.133][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:53.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:53.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:53.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:53.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:53.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:53.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:53.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.179][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:53.198][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:53.205][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:53.208][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-04-15 23:57:53.212][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:53.215][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-04-15 23:57:53.220][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:53.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:53.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:53.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:53.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:53.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:53.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:53.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.267][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:53.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:53.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:53.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:53.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:53.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:53.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:53.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:53.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:53.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:53.349][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 23:57:53.352][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:53.354][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:53.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:53.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:53.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:53.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:53.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:53.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.415][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.418][private$selectFields]
biodb.TRACE[2024-04-15 23:57:53.420][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:53.422][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:53.424][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.426][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.428][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.430][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.431][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.433][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.437][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.440][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.441][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.443][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.444][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.448][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.452][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.454][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:53.456][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.525][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-04-15 23:57:53.527][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:53.537][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:53.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:53.602][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:53.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:53.606][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:53.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:53.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.627][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.629][private$selectFields]
biodb.TRACE[2024-04-15 23:57:53.631][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:53.633][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:53.636][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.639][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.641][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.643][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.646][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.648][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.650][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.659][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.661][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.663][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.666][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.671][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.675][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.678][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:53.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.710][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-15 23:57:53.713][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:53.714][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:53.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:53.797][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:53.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:53.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:53.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:53.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.824][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.826][private$selectFields]
biodb.TRACE[2024-04-15 23:57:53.829][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:53.831][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:53.834][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.836][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.838][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.846][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.848][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.849][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.851][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.855][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.857][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.859][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:53.861][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.863][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.866][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.868][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.870][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:53.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.900][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-04-15 23:57:53.902][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 23:57:53.904][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 23:57:53.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:53.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:53.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:53.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:54.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:54.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:54.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:54.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:54.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:54.143][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:54.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:54.151][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:54.208][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:54.210][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:54.215][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:57:54.601][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:57:54.986][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:54.990][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-04-15 23:57:55.015][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-04-15 23:57:55.022][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:55.029][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:57:55.031][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:57:55.035][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:57:55.420][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:57:55.803][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:57:55.808][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-04-15 23:57:55.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-04-15 23:57:55.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:55.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:55.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:55.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:55.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:55.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:55.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:55.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:55.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:55.870][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:55.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:55.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:55.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:55.890][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:55.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:55.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:55.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:55.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:55.966][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:55.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:55.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:55.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:55.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:55.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:55.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:55.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:56.002][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:56.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:56.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:56.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:56.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:56.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:56.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:56.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:56.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:56.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:56.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:56.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:56.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:56.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:56.114][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 23:57:56.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:56.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:56.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:56.204][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:56.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:56.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:56.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:56.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.233][private$selectFields]
biodb.TRACE[2024-04-15 23:57:56.235][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:56.237][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:56.239][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.242][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.259][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.264][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.269][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.273][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.276][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.278][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.283][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.287][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.289][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:56.291][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.310][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.320][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-04-15 23:57:56.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:56.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:56.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:56.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:56.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:56.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:56.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:56.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.443][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.445][private$selectFields]
biodb.TRACE[2024-04-15 23:57:56.465][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:56.467][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:56.470][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.472][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.474][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.478][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.481][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.483][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.485][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.487][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.489][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.516][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.519][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.521][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.524][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.526][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.528][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:56.530][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.540][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.558][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-15 23:57:56.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:56.564][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:56.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:56.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:56.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:56.595][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:56.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:56.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.625][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.627][private$selectFields]
biodb.TRACE[2024-04-15 23:57:56.629][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:56.632][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:56.633][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.635][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.642][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.644][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.646][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.648][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.650][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.653][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.655][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:56.673][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.676][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.680][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.682][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:56.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:56.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.711][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-04-15 23:57:56.713][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 23:57:56.715][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 23:57:56.734][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 23:57:56.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 23:57:56.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:56.751][biodb::testThat]
biodb.INFO [2024-04-15 23:57:56.753][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-04-15 23:57:56.755][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:56.757][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:56.762][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 23:57:56.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 23:57:56.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.775][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.798][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:56.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:56.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:56.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:56.835][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:56.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:56.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:56.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:56.847][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:56.868][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:56.871][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-04-15 23:57:56.874][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:56.877][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-04-15 23:57:56.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:56.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:56.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:56.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:56.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:56.920][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:56.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:56.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:56.944][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:56.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:56.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:56.956][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:56.966][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:56.971][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-04-15 23:57:56.974][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:56.977][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-04-15 23:57:56.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:56.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:56.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:56.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.007][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:57.035][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:57.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:57.146][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 23:57:57.150][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.169][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.181][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.197][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.206][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.209][private$selectFields]
biodb.TRACE[2024-04-15 23:57:57.211][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:57.213][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:57.215][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.218][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.220][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.224][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.227][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.234][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.236][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.238][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.255][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.258][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.263][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.265][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:57.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.293][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-04-15 23:57:57.296][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.300][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.337][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.340][private$selectFields]
biodb.TRACE[2024-04-15 23:57:57.342][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:57.344][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:57.346][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.350][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.353][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.363][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.365][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.367][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.375][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.377][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.382][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.384][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.387][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.389][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.391][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.394][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:57.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-15 23:57:57.445][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.449][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.500][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.524][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.525][private$selectFields]
biodb.TRACE[2024-04-15 23:57:57.527][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:57.529][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:57.531][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.533][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.535][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.539][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.541][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.543][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.547][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.549][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.551][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.559][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.564][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.566][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:57.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.599][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-04-15 23:57:57.601][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 23:57:57.603][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 23:57:57.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.644][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.653][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:57.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.700][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:57.708][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:57.715][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:57.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-04-15 23:57:57.720][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:57.724][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-04-15 23:57:57.730][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:57.738][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:57.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-04-15 23:57:57.742][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:57.748][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-04-15 23:57:57.752][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.769][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:57.804][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.806][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.822][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:57.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.865][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.867][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:57.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:57.917][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 23:57:57.920][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:57.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:57.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:57.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:57.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:57.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:57.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:57.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.967][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.969][private$selectFields]
biodb.TRACE[2024-04-15 23:57:57.971][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:57.974][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:57.976][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.978][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.981][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.983][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.985][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.987][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.990][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:57.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:57.994][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:57.996][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:57.999][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.015][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.017][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.021][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.023][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:58.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.052][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-04-15 23:57:58.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.074][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:58.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.096][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.100][private$selectFields]
biodb.TRACE[2024-04-15 23:57:58.102][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:58.104][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:58.111][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.114][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.117][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.122][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.125][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.127][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.130][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.133][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.136][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.139][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.142][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.144][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.147][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.152][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.154][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:58.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.219][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-15 23:57:58.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.225][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:58.247][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.264][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.266][private$selectFields]
biodb.TRACE[2024-04-15 23:57:58.268][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:58.270][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:58.272][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.274][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.276][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.278][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.279][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.280][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.281][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.285][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.287][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.288][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.290][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.291][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.295][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.297][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:58.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.316][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.337][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-04-15 23:57:58.339][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 23:57:58.342][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 23:57:58.360][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 23:57:58.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 23:57:58.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 23:57:58.375][biodb::testThat]
biodb.INFO [2024-04-15 23:57:58.378][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-04-15 23:57:58.380][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:57:58.382][biodb::testThat]
biodb.TRACE[2024-04-15 23:57:58.387][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-04-15 23:57:58.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-04-15 23:57:58.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:58.458][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.460][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.462][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.472][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:58.484][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:58.490][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:58.493][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-04-15 23:57:58.495][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:58.503][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-04-15 23:57:58.507][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.529][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:58.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.542][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.551][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:58.562][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:58.569][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:58.572][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-04-15 23:57:58.575][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:58.578][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-04-15 23:57:58.582][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.664][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:58.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.678][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:58.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.712][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.731][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:58.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:57:58.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:58.761][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 23:57:58.764][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:58.800][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.814][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.816][private$selectFields]
biodb.TRACE[2024-04-15 23:57:58.818][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:58.820][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:58.821][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.823][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.826][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.829][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.831][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.833][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.835][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.838][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.840][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.843][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.845][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.847][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.850][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.851][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:58.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.867][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.876][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-04-15 23:57:58.878][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:58.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:58.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:58.902][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:58.906][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:58.908][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:58.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:58.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.930][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.932][private$selectFields]
biodb.TRACE[2024-04-15 23:57:58.934][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:58.936][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:58.938][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.941][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.943][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.947][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.949][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.952][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.956][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.959][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.961][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:58.964][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.967][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:58.971][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:58.990][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:58.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.020][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-15 23:57:59.022][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:59.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.076][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.078][private$selectFields]
biodb.TRACE[2024-04-15 23:57:59.080][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:59.082][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:59.089][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.091][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.093][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.101][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.103][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.106][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.110][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.112][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.115][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.117][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.119][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.122][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.124][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:59.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.152][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-04-15 23:57:59.155][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 23:57:59.157][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 23:57:59.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:59.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:57:59.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:59.345][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:59.347][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-04-15 23:57:59.350][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:59.353][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-04-15 23:57:59.359][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:57:59.366][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:57:59.370][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-04-15 23:57:59.373][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:57:59.376][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-04-15 23:57:59.380][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.382][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.384][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.394][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.398][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:59.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.422][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:59.441][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.443][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.445][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:59.471][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:59.494][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.501][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:59.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.545][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:57:59.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:57:59.554][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 23:57:59.558][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.560][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.573][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.577][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.579][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:59.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.616][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.618][private$selectFields]
biodb.TRACE[2024-04-15 23:57:59.620][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:59.621][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:59.624][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.626][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.629][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.631][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.633][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.636][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.638][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.642][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.645][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.647][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.649][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.652][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.656][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.659][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:59.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.699][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-04-15 23:57:59.703][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.724][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:59.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.738][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.747][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.749][private$selectFields]
biodb.TRACE[2024-04-15 23:57:59.751][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:59.753][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:59.756][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.758][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.760][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.762][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.765][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.767][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.770][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.774][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.776][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.778][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.793][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.796][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.801][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.803][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:59.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.815][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.834][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-04-15 23:57:59.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:57:59.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:57:59.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:57:59.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:57:59.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:57:59.855][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:57:59.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:57:59.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.877][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.879][private$selectFields]
biodb.TRACE[2024-04-15 23:57:59.882][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-04-15 23:57:59.884][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-04-15 23:57:59.886][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.889][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.892][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.896][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.898][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.901][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.905][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.907][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.910][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-04-15 23:57:59.912][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.915][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.917][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.924][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.926][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-04-15 23:57:59.928][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:57:59.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:57:59.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:57:59.960][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-04-15 23:57:59.963][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 23:57:59.965][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-04-15 23:58:00.052][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-04-15 23:58:00.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-04-15 23:58:00.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:00.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-04-15 23:58:00.069][biodb::testThat]
biodb.INFO [2024-04-15 23:58:00.070][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-04-15 23:58:00.072][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:00.075][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:00.078][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-04-15 23:58:00.080][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:58:00.084][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-04-15 23:58:00.090][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:58:00.092][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:58:00.094][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:58:00.096][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:58:00.102][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:58:00.105][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:58:00.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:00.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:00.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:00.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:00.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:00.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:00.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:00.134][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-04-15 23:58:00.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:00.142][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:00.145][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-04-15 23:58:00.527][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-04-15 23:58:00.914][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:00.918][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-04-15 23:58:00.926][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-04-15 23:58:00.932][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-04-15 23:58:00.936][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:58:00.938][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:58:00.941][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:58:00.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:00.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:00.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.021][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.028][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[2024-04-15 23:58:01.033][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.036][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.038][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.040][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.052][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:01.055][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:01.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.061][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.064][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:01.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:01.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.070][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.073][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:58:01.076][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:58:01.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.081][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.088][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:58:01.090][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:58:01.092][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.094][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.101][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:01.103][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:01.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.107][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.111][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:01.113][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:01.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.117][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.120][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:01.122][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:01.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.126][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.128][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:01.130][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:01.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.134][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.137][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:01.140][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:01.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.144][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.146][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:01.149][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:01.151][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.153][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:01.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:01.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.166][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:01.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:01.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.192][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.200][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:01.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:01.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:01.254][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:01.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:01.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:01.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:58:01.263][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-04-15 23:58:01.266][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-15 23:58:01.284][biodb::testThat]
biodb.INFO [2024-04-15 23:58:01.291][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-04-15 23:58:01.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:01.295][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:01.320][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-04-15 23:58:01.323][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-04-15 23:58:01.325][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-04-15 23:58:01.330][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-04-15 23:58:01.333][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-04-15 23:58:01.336][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:58:01.339][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:58:01.341][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:58:01.344][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:58:01.346][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:58:01.355][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:01.372][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:01.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:01.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:01.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:01.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:01.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:01.442][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-04-15 23:58:01.447][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:01.450][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:01.453][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-04-15 23:58:01.837][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-04-15 23:58:02.218][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:02.222][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-04-15 23:58:02.230][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-04-15 23:58:02.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:02.235][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:02.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:02.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:02.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:02.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:02.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:02.259][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-04-15 23:58:02.268][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:02.271][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:02.274][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-04-15 23:58:02.656][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-04-15 23:58:03.065][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:03.070][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-04-15 23:58:03.099][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-04-15 23:58:03.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:03.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:03.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:03.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:03.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:03.165][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:03.167][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[2024-04-15 23:58:03.169][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-04-15 23:58:03.175][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:03.178][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:03.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-04-15 23:58:03.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-04-15 23:58:03.952][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:03.956][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-04-15 23:58:03.964][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-04-15 23:58:03.970][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-04-15 23:58:03.976][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:58:03.979][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-04-15 23:58:03.982][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-04-15 23:58:03.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:03.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:03.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:04.000][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:04.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:04.004][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:04.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:04.011][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.013][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.016][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.034][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:04.037][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:04.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.041][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.044][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:04.047][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:04.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.051][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.054][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:58:04.056][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:58:04.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.060][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.063][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.065][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.070][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.072][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.075][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.077][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.079][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.081][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:04.084][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:04.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.088][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.091][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.093][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.111][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.114][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:04.115][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:04.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.119][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.121][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:04.124][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:04.125][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.126][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.127][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:04.129][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:04.130][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.131][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:58:04.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:04.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:04.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:04.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:04.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:04.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:04.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:04.217][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.220][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.224][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.238][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:04.240][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:04.244][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.246][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.249][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:04.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:04.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.259][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:04.261][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:04.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.266][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.269][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:04.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:04.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:58:04.281][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:58:04.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.286][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:58:04.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:58:04.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.310][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.313][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.315][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.318][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.321][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.331][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.334][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.339][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.352][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.368][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:04.371][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:04.373][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.375][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.378][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:04.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:04.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.388][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.390][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.394][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.406][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:04.409][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:04.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.413][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:04.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:04.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.434][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:04.436][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:04.438][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.440][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.443][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:04.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:04.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.452][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:04.455][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:04.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.459][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.462][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:04.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:04.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:58:04.549][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:04.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:04.569][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:04.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:04.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:04.584][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:04.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:04.591][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.593][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.598][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.600][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.609][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:04.612][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:04.614][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.616][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.620][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:04.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:04.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.628][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:04.630][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:04.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.634][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.643][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:04.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:04.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.655][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:58:04.658][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:58:04.660][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.664][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:58:04.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:58:04.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.677][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.680][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.685][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:58:04.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.697][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.700][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.714][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.716][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.719][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:04.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.727][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:04.730][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:04.731][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.733][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.736][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:04.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.745][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.747][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.751][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.757][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:04.759][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:04.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.761][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:04.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.774][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:04.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:04.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.780][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:04.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:04.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.789][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:04.791][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:04.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.795][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.797][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:04.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:04.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:04.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:04.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:04.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:04.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:58:04.983][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-04-15 23:58:04.985][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-15 23:58:04.987][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-04-15 23:58:05.019][biodb::testThat]
biodb.INFO [2024-04-15 23:58:05.021][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-04-15 23:58:05.028][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:05.031][biodb::testThat]
biodb.INFO [2024-04-15 23:58:05.087][biodb::testThat]
biodb.INFO [2024-04-15 23:58:05.089][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-04-15 23:58:05.092][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:05.094][biodb::testThat]
biodb.INFO [2024-04-15 23:58:05.113][biodb::testThat]
biodb.INFO [2024-04-15 23:58:05.129][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-04-15 23:58:05.131][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:05.133][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:05.138][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:05.173][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:05.175][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:05.181][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:58:05.631][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:58:06.166][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:06.174][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-04-15 23:58:06.192][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-04-15 23:58:06.223][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:06.225][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:06.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:06.230][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:06.232][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:06.233][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:06.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:06.238][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 23:58:06.241][biodb::testThat]
biodb.INFO [2024-04-15 23:58:06.244][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-04-15 23:58:06.246][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:06.248][biodb::testThat]
biodb.ERROR[2024-04-15 23:58:06.275][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-04-15 23:58:06.335][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-04-15 23:58:06.364][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 23:58:06.366][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-15 23:58:06.368][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-15 23:58:06.371][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 23:58:06.373][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:06.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:06.377][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:06.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:06.381][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 23:58:06.407][biodb::testContext]
biodb.INFO [2024-04-15 23:58:06.410][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:06.413][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-04-15 23:58:06.415][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:06.417][biodb::testContext]
biodb.INFO [2024-04-15 23:58:06.422][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:06.425][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:06.432][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:06.435][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 23:58:06.437][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 23:58:06.439][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.446][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.448][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 23:58:06.450][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 23:58:06.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.458][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 23:58:06.477][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 23:58:06.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.481][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.485][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 23:58:06.488][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 23:58:06.490][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 23:58:06.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.497][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[2024-04-15 23:58:06.499][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 23:58:06.501][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 23:58:06.503][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 23:58:06.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.509][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 23:58:06.511][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 23:58:06.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.518][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 23:58:06.521][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 23:58:06.524][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 23:58:06.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.534][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 23:58:06.536][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 23:58:06.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.542][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 23:58:06.545][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 23:58:06.547][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 23:58:06.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.555][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:06.557][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 23:58:06.559][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 23:58:06.562][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 23:58:06.565][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 23:58:06.567][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 23:58:06.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.575][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 23:58:06.578][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 23:58:06.579][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.584][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 23:58:06.586][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 23:58:06.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.600][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 23:58:06.602][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 23:58:06.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.614][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 23:58:06.618][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 23:58:06.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.626][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 23:58:06.628][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 23:58:06.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.636][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:06.639][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 23:58:06.655][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 23:58:06.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.662][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 23:58:06.664][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 23:58:06.666][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 23:58:06.668][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.673][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 23:58:06.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.678][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 23:58:06.680][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.683][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:06.685][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.688][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.691][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.693][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.696][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:06.698][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:06.701][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.703][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 23:58:06.705][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:06.708][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.710][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.712][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:06.712][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:06.712][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:06.712][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:06.712][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:06.714][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:06.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.720][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:06.722][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.724][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.726][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.728][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.730][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:06.732][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:06.733][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.736][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.739][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 23:58:06.742][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.743][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:06.745][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.755][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:06.757][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.760][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.765][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.772][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:06.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:06.776][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.778][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 23:58:06.780][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:06.782][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.784][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.790][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:06.790][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:06.790][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:06.790][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:06.790][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:06.792][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:06.794][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.796][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.800][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:06.802][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.809][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.811][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:06.813][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:06.816][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.818][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.820][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 23:58:06.825][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.838][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 23:58:06.840][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.842][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:06.844][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.845][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.847][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.850][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:06.851][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:06.853][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.854][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 23:58:06.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:06.856][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.858][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.859][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.860][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:06.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.863][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.864][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:06.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.868][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.869][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.871][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:06.872][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:06.873][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.875][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.877][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 23:58:06.881][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.883][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:06.886][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.888][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:06.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.894][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.896][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.898][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:06.900][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:06.902][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.904][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 23:58:06.905][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:06.908][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.910][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:06.912][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.915][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:06.917][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.919][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.921][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:06.923][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:06.925][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:06.927][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:06.930][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.932][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:06.933][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:06.935][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:06.937][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:06.940][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:06.942][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.944][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[2024-04-15 23:58:06.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:06.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:06.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.951][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[2024-04-15 23:58:06.960][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:06.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:06.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.968][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[2024-04-15 23:58:06.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:06.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:06.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:06.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:06.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:06.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:06.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:06.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:06.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:06.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.011][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[2024-04-15 23:58:07.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.033][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.039][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.041][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.113][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[2024-04-15 23:58:07.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.125][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[2024-04-15 23:58:07.127][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.137][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 23:58:07.140][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 23:58:07.145][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 23:58:07.148][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 23:58:07.151][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:07.159][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 23:58:07.162][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:07.174][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:07.177][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 23:58:07.181][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 23:58:07.185][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:07.188][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 23:58:07.192][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:07.195][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:07.198][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 23:58:07.202][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:58:07.205][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 23:58:07.222][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 23:58:07.225][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:07.229][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 23:58:07.232][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 23:58:07.236][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 23:58:07.240][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 23:58:07.243][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 23:58:07.245][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 23:58:07.260][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 23:58:07.265][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 23:58:07.269][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 23:58:07.272][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 23:58:07.276][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 23:58:07.280][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 23:58:07.283][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 23:58:07.287][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 23:58:07.291][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 23:58:07.294][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 23:58:07.297][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 23:58:07.300][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 23:58:07.303][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 23:58:07.307][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 23:58:07.310][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 23:58:07.311][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 23:58:07.313][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 23:58:07.317][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 23:58:07.321][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 23:58:07.330][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 23:58:07.333][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 23:58:07.336][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 23:58:07.344][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 23:58:07.347][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 23:58:07.350][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 23:58:07.353][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 23:58:07.356][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 23:58:07.359][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 23:58:07.363][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 23:58:07.366][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 23:58:07.370][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 23:58:07.376][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 23:58:07.379][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 23:58:07.382][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 23:58:07.387][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 23:58:07.390][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 23:58:07.393][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 23:58:07.397][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 23:58:07.401][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 23:58:07.420][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 23:58:07.423][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 23:58:07.426][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:07.431][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:07.434][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 23:58:07.438][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 23:58:07.441][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 23:58:07.444][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 23:58:07.448][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 23:58:07.451][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 23:58:07.454][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 23:58:07.458][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 23:58:07.461][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 23:58:07.464][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 23:58:07.468][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 23:58:07.474][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 23:58:07.477][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 23:58:07.481][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 23:58:07.485][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 23:58:07.488][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 23:58:07.492][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:07.494][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:07.496][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.500][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.502][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[2024-04-15 23:58:07.505][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.541][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.557][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.623][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.756][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.DEBUG[2024-04-15 23:58:07.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.804][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.808][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.827][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.831][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.845][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[2024-04-15 23:58:07.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.866][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.975][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:07.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:07.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:07.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:07.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:07.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:07.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:07.998][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:08.002][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-15 23:58:08.006][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:08.010][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 23:58:08.012][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:08.016][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:08.018][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:08.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:08.023][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:08.026][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-15 23:58:08.028][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-15 23:58:08.031][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:08.033][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:08.036][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-15 23:58:08.039][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-15 23:58:08.041][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-15 23:58:08.053][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:08.055][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:08.055][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:08.055][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:08.058][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-15 23:58:08.060][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:08.069][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:08.071][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:08.073][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:08.075][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:08.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:08.079][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:58:08.079][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-15 23:58:08.082][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:08.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:08.088][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:08.091][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-15 23:58:08.091][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-15 23:58:08.094][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:08.098][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:08.101][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-15 23:58:08.105][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:08.127][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:08.175][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:08.183][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-15 23:58:08.185][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-15 23:58:08.187][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-15 23:58:08.191][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-15 23:58:08.193][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:58:08.195][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:58:08.198][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-15 23:58:08.200][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-15 23:58:08.203][biodb::testThat]
biodb.INFO [2024-04-15 23:58:08.205][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-04-15 23:58:08.208][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:08.212][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:08.219][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-15 23:58:08.227][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:08.231][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-04-15 23:58:08.234][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:08.237][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-04-15 23:58:08.245][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:08.258][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:08.260][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:08.264][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:58:08.655][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:58:09.100][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:09.104][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-04-15 23:58:09.117][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-04-15 23:58:09.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:09.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:09.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:09.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:09.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:09.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:09.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:09.166][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:09.174][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:09.175][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:09.180][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:58:09.563][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:58:09.946][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:09.957][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-04-15 23:58:10.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-04-15 23:58:10.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:10.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:10.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:10.034][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:10.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:10.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:10.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:10.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:10.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:10.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:10.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:10.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:10.124][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:10.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:10.137][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:10.145][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:10.148][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-04-15 23:58:10.151][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:10.154][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-04-15 23:58:10.189][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:10.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:10.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:10.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:10.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:10.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:10.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:10.262][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:10.269][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:10.272][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-04-15 23:58:10.277][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:10.280][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-04-15 23:58:10.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:10.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:10.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:10.299][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:10.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:10.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:10.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:10.308][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:10.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:10.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:10.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:10.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:10.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:10.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:10.339][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:10.347][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:10.350][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-04-15 23:58:10.353][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:10.357][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-04-15 23:58:10.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:10.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:10.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:10.377][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:10.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:10.381][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:10.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:10.388][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:10.397][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:10.438][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-04-15 23:58:10.474][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:10.484][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-04-15 23:58:10.488][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:10.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:10.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:10.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:10.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:10.504][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:10.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:10.511][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:10.520][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:10.522][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:10.526][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:58:10.908][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:58:11.287][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:11.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-04-15 23:58:11.318][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-04-15 23:58:11.322][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:11.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:11.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:11.337][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:11.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:11.341][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:11.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 23:58:11.364][biodb::testThat]
biodb.INFO [2024-04-15 23:58:11.366][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-04-15 23:58:11.368][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:11.371][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:11.382][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:11.390][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:11.392][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:11.397][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:58:11.783][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:58:12.166][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:12.171][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-04-15 23:58:12.186][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-04-15 23:58:12.191][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:12.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:12.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:12.243][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:12.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:12.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:12.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:12.286][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:12.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:12.296][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:12.300][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:58:12.681][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:58:13.069][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:13.073][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-04-15 23:58:13.083][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-04-15 23:58:13.088][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:13.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:13.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:13.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.108][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 23:58:13.124][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 23:58:13.127][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-15 23:58:13.129][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-15 23:58:13.132][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 23:58:13.134][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:13.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:13.137][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:13.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:13.163][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 23:58:13.217][biodb::testContext]
biodb.INFO [2024-04-15 23:58:13.220][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:13.222][biodb::testContext] Test context - Test web services
biodb.INFO [2024-04-15 23:58:13.225][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:13.227][biodb::testContext]
biodb.INFO [2024-04-15 23:58:13.231][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:13.237][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:13.245][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:13.248][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 23:58:13.256][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.262][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[2024-04-15 23:58:13.270][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 23:58:13.273][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.281][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 23:58:13.284][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.294][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 23:58:13.296][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 23:58:13.299][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 23:58:13.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.307][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 23:58:13.310][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 23:58:13.312][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.321][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 23:58:13.324][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 23:58:13.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.333][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 23:58:13.335][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 23:58:13.337][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 23:58:13.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.345][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 23:58:13.348][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.355][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 23:58:13.370][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 23:58:13.411][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 23:58:13.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.421][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:13.423][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 23:58:13.426][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 23:58:13.428][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 23:58:13.430][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 23:58:13.433][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 23:58:13.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.441][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 23:58:13.443][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 23:58:13.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.449][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.DEBUG[2024-04-15 23:58:13.452][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 23:58:13.455][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 23:58:13.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.467][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 23:58:13.470][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 23:58:13.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.483][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 23:58:13.487][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 23:58:13.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.495][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 23:58:13.498][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 23:58:13.500][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.506][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:13.508][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 23:58:13.534][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 23:58:13.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.542][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 23:58:13.544][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 23:58:13.547][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 23:58:13.558][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:13.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:13.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:13.567][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 23:58:13.572][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.574][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 23:58:13.576][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.579][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:13.581][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.583][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.585][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.587][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.590][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:13.592][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:13.594][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.596][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 23:58:13.598][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:13.601][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.603][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.605][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:13.605][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:13.605][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:13.605][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:13.605][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:13.801][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:13.804][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.808][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:13.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.814][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.816][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.818][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:13.820][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:13.821][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.823][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.826][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 23:58:13.830][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.832][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:13.837][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.839][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:13.842][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.844][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.851][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.853][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.855][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:13.857][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:13.859][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.862][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 23:58:13.864][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:13.865][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.867][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.869][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:13.869][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:13.869][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:13.869][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:13.869][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:13.872][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:13.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.878][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:13.880][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.887][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.889][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:13.890][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:13.893][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.895][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.898][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 23:58:13.902][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.905][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 23:58:13.907][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.910][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:13.912][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.915][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.917][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.920][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.922][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:13.924][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:13.927][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:13.929][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 23:58:13.932][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:13.934][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.937][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:13.952][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:13.955][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:13.957][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.958][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.960][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:13.963][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:13.965][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:13.967][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:13.969][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:14.004][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:14.006][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:14.008][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:14.010][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:14.019][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 23:58:14.023][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.025][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:14.027][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.030][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:14.032][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.034][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:14.036][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:14.038][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:14.040][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:14.043][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:14.045][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:14.057][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 23:58:14.059][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:14.062][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:14.066][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:14.073][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:14.075][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:14.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:14.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:14.080][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:14.083][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:14.085][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:14.087][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:14.089][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:14.091][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:14.093][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:14.095][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:14.097][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:14.100][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:14.101][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.130][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.210][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.243][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.319][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.331][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.361][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.433][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[2024-04-15 23:58:14.436][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 23:58:14.446][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 23:58:14.450][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 23:58:14.453][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 23:58:14.457][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:14.465][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 23:58:14.468][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:14.471][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:14.478][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 23:58:14.481][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 23:58:14.485][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:14.488][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 23:58:14.491][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:14.494][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:14.497][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 23:58:14.501][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:58:14.504][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 23:58:14.508][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 23:58:14.511][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:14.515][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 23:58:14.518][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 23:58:14.521][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 23:58:14.524][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 23:58:14.528][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 23:58:14.531][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 23:58:14.534][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 23:58:14.537][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 23:58:14.541][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 23:58:14.544][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 23:58:14.547][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 23:58:14.550][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 23:58:14.567][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 23:58:14.570][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 23:58:14.612][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 23:58:14.616][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 23:58:14.620][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 23:58:14.623][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 23:58:14.626][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 23:58:14.629][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 23:58:14.633][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 23:58:14.637][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 23:58:14.641][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 23:58:14.644][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 23:58:14.648][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 23:58:14.652][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 23:58:14.655][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 23:58:14.659][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 23:58:14.663][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 23:58:14.666][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 23:58:14.672][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 23:58:14.675][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 23:58:14.677][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 23:58:14.680][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 23:58:14.691][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 23:58:14.705][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 23:58:14.714][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 23:58:14.717][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 23:58:14.720][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 23:58:14.724][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 23:58:14.727][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 23:58:14.730][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 23:58:14.733][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 23:58:14.736][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 23:58:14.740][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 23:58:14.743][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 23:58:14.747][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 23:58:14.750][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:14.753][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:14.756][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 23:58:14.759][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 23:58:14.775][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 23:58:14.778][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 23:58:14.814][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 23:58:14.817][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 23:58:14.821][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 23:58:14.824][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 23:58:14.827][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 23:58:14.831][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 23:58:14.834][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 23:58:14.837][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 23:58:14.841][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 23:58:14.844][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 23:58:14.848][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 23:58:14.851][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 23:58:14.853][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:14.856][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:14.858][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.862][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.879][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.900][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[2024-04-15 23:58:14.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.917][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[2024-04-15 23:58:14.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.933][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:14.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:14.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:14.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:14.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:14.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:14.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:14.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.026][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.045][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[2024-04-15 23:58:15.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.068][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.100][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.119][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.134][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.146][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[2024-04-15 23:58:15.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.152][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.164][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.246][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.DEBUG[2024-04-15 23:58:15.248][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:15.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:15.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:15.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:15.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:15.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:15.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:15.264][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:15.266][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-15 23:58:15.270][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:15.272][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 23:58:15.274][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:15.276][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:15.278][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:15.280][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:15.282][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:15.284][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-15 23:58:15.287][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-15 23:58:15.289][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:15.297][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:15.300][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-15 23:58:15.302][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-15 23:58:15.304][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-15 23:58:15.306][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:15.313][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:15.313][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:15.313][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:15.315][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-15 23:58:15.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:15.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:15.321][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:15.324][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:15.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:15.328][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:15.330][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:58:15.330][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-15 23:58:15.333][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:15.335][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:15.337][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:15.339][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-15 23:58:15.339][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-15 23:58:15.343][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:15.346][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:15.351][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-15 23:58:15.355][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:15.358][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:15.362][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:15.380][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-15 23:58:15.415][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-15 23:58:15.418][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-15 23:58:15.422][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-15 23:58:15.425][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:58:15.433][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:58:15.436][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-15 23:58:15.438][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-15 23:58:15.441][biodb::testThat]
biodb.INFO [2024-04-15 23:58:15.443][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-04-15 23:58:15.445][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:15.447][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:15.453][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-15 23:58:15.460][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:15.464][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-04-15 23:58:15.467][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:15.469][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-04-15 23:58:15.477][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:15.485][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:15.487][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:15.491][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-04-15 23:58:15.887][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-04-15 23:58:16.270][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:16.274][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-04-15 23:58:16.283][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-04-15 23:58:16.312][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 23:58:16.348][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-15 23:58:16.351][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-15 23:58:16.353][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 23:58:16.356][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:16.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:16.361][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:16.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:16.365][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 23:58:16.375][biodb::testContext]
biodb.INFO [2024-04-15 23:58:16.377][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:16.379][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-04-15 23:58:16.381][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 23:58:16.383][biodb::testContext]
biodb.INFO [2024-04-15 23:58:16.388][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:16.391][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:16.400][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:16.402][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 23:58:16.404][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 23:58:16.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.416][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 23:58:16.418][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 23:58:16.423][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.427][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.DEBUG[2024-04-15 23:58:16.429][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 23:58:16.432][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 23:58:16.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.440][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 23:58:16.443][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 23:58:16.445][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 23:58:16.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.467][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 23:58:16.469][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 23:58:16.480][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 23:58:16.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.529][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 23:58:16.531][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 23:58:16.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.537][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[2024-04-15 23:58:16.539][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 23:58:16.541][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 23:58:16.543][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 23:58:16.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.552][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 23:58:16.554][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 23:58:16.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.563][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 23:58:16.565][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 23:58:16.567][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 23:58:16.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.572][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.574][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.577][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:16.579][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 23:58:16.581][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 23:58:16.582][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 23:58:16.584][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 23:58:16.592][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 23:58:16.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.601][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 23:58:16.607][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 23:58:16.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.615][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 23:58:16.618][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 23:58:16.620][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.626][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 23:58:16.629][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 23:58:16.631][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.637][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 23:58:16.640][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 23:58:16.643][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.649][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 23:58:16.652][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 23:58:16.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.661][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 23:58:16.663][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 23:58:16.681][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 23:58:16.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.744][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 23:58:16.747][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 23:58:16.749][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 23:58:16.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:16.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:16.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:16.758][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 23:58:16.762][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.765][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 23:58:16.767][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.770][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:16.773][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.775][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.778][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.780][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.783][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:16.785][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:16.788][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.790][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 23:58:16.792][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:16.794][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:16.796][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.799][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:16.799][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:16.799][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:16.799][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:16.799][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:16.808][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:16.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:16.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:16.814][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:16.822][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:16.824][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:16.825][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.828][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:16.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:16.834][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:16.836][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.838][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:16.841][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 23:58:16.845][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.847][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:16.850][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.852][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:16.854][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.856][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.859][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.861][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.863][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:16.865][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:16.868][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.871][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 23:58:16.873][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:16.875][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:16.890][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.893][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:16.893][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:16.893][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:16.893][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 23:58:16.893][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 23:58:16.896][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:16.935][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:16.937][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:16.939][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:16.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:16.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:16.945][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.947][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:16.949][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:16.951][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:16.953][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.955][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:16.957][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 23:58:16.960][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.962][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 23:58:16.965][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.968][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:16.970][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.972][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.974][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.976][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:16.978][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 23:58:16.981][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:16.983][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:16.986][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 23:58:16.988][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:16.990][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:16.992][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:16.994][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:17.003][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:17.005][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:17.007][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:17.009][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:17.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:17.017][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:17.019][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:17.020][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:17.024][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:17.026][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:17.028][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:17.031][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:17.033][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 23:58:17.037][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:17.039][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 23:58:17.042][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:17.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:17.046][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:17.048][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:17.050][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:17.052][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 23:58:17.055][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 23:58:17.057][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:17.059][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:17.061][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 23:58:17.063][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:17.065][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:17.067][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:17.083][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:17.087][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 23:58:17.131][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:17.140][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:17.143][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:17.145][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:17.147][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:17.148][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:17.150][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:17.152][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:17.154][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:17.156][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:17.158][self$setPropertyValue]
biodb.DEBUG[2024-04-15 23:58:17.161][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:17.171][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.180][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[2024-04-15 23:58:17.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.232][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.250][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.257][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.DEBUG[2024-04-15 23:58:17.259][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.372][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.DEBUG[2024-04-15 23:58:17.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.382][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[2024-04-15 23:58:17.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.420][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[2024-04-15 23:58:17.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.431][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.441][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 23:58:17.444][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 23:58:17.447][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 23:58:17.450][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 23:58:17.453][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:17.456][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 23:58:17.460][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:17.463][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:17.466][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 23:58:17.470][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 23:58:17.473][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:17.476][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 23:58:17.479][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 23:58:17.481][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 23:58:17.484][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 23:58:17.488][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 23:58:17.491][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 23:58:17.494][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 23:58:17.496][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:17.498][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 23:58:17.499][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 23:58:17.501][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 23:58:17.504][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 23:58:17.507][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 23:58:17.509][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 23:58:17.512][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 23:58:17.515][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 23:58:17.518][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 23:58:17.520][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 23:58:17.524][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 23:58:17.527][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 23:58:17.530][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 23:58:17.533][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 23:58:17.537][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 23:58:17.540][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 23:58:17.543][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 23:58:17.546][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 23:58:17.549][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 23:58:17.552][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 23:58:17.554][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 23:58:17.557][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 23:58:17.560][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 23:58:17.563][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 23:58:17.565][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 23:58:17.568][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 23:58:17.571][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 23:58:17.574][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 23:58:17.578][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 23:58:17.581][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 23:58:17.584][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 23:58:17.588][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 23:58:17.591][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 23:58:17.594][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 23:58:17.597][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 23:58:17.620][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 23:58:17.665][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 23:58:17.668][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 23:58:17.671][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 23:58:17.674][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 23:58:17.677][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 23:58:17.681][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 23:58:17.691][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 23:58:17.694][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 23:58:17.697][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 23:58:17.701][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 23:58:17.703][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 23:58:17.706][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:17.716][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:17.719][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 23:58:17.725][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 23:58:17.728][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 23:58:17.732][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 23:58:17.735][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 23:58:17.737][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 23:58:17.739][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 23:58:17.741][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 23:58:17.743][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 23:58:17.746][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 23:58:17.749][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 23:58:17.752][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 23:58:17.755][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 23:58:17.758][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 23:58:17.762][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 23:58:17.765][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 23:58:17.768][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 23:58:17.770][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 23:58:17.772][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.776][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.895][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.938][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.957][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.961][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.963][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.968][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[2024-04-15 23:58:17.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:17.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:17.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:17.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:17.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:17.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:17.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:17.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.011][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[2024-04-15 23:58:18.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:18.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.022][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:18.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:18.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:18.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:18.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.064][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:18.073][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:18.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:18.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:18.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:18.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 23:58:18.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:18.121][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-04-15 23:58:18.124][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-04-15 23:58:18.128][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:18.131][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 23:58:18.133][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:18.135][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 23:58:18.137][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:18.139][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 23:58:18.141][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:18.143][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-04-15 23:58:18.145][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-04-15 23:58:18.147][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 23:58:18.150][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:18.152][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-04-15 23:58:18.154][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-04-15 23:58:18.156][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-04-15 23:58:18.159][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 23:58:18.161][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 23:58:18.161][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 23:58:18.161][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 23:58:18.164][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-04-15 23:58:18.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:18.168][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:18.170][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 23:58:18.172][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 23:58:18.183][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 23:58:18.219][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 23:58:18.222][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:58:18.222][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-04-15 23:58:18.224][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 23:58:18.226][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 23:58:18.229][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 23:58:18.231][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-04-15 23:58:18.231][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-04-15 23:58:18.241][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 23:58:18.244][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 23:58:18.247][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-04-15 23:58:18.250][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 23:58:18.253][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 23:58:18.256][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 23:58:18.265][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-04-15 23:58:18.268][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-04-15 23:58:18.278][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-04-15 23:58:18.281][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-04-15 23:58:18.284][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:58:18.287][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-04-15 23:58:18.290][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-04-15 23:58:18.292][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-04-15 23:58:18.295][biodb::testThat]
biodb.INFO [2024-04-15 23:58:18.298][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-04-15 23:58:18.300][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 23:58:18.302][biodb::testThat]
biodb.DEBUG[2024-04-15 23:58:18.309][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-04-15 23:58:18.317][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:18.319][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-04-15 23:58:18.322][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:18.325][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-04-15 23:58:18.332][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-04-15 23:58:18.350][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 23:58:18.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-04-15 23:58:18.395][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 23:58:18.398][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-04-15 23:58:18.407][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-04-15 23:58:18.410][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 23:58:18.413][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-04-15 23:58:18.419][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-04-15 23:58:18.421][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-04-15 23:58:18.425][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 23:58:18.427][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-04-15 23:58:18.429][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-04-15 23:58:18.431][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-04-15 23:58:18.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:18.439][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:18.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:18.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:18.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:18.461][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:18.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 23:58:18.465][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-04-15 23:58:18.471][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-04-15 23:58:18.473][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-04-15 23:58:18.476][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-04-15 23:58:18.867][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-04-15 23:58:19.617][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-04-15 23:58:19.630][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-04-15 23:58:19.639][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-04-15 23:58:19.645][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-04-15 23:58:19.652][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-04-15 23:58:19.655][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-04-15 23:58:19.658][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-04-15 23:58:19.662][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 23:58:19.664][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:19.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:19.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:19.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:19.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:19.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 23:58:19.693][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:19.695][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:19.697][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.699][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:19.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:19.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.768][ef$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:19.770][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:19.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.774][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.776][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-04-15 23:58:19.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-04-15 23:58:19.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.787][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:19.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:19.791][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.793][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.795][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 23:58:19.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 23:58:19.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.804][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-04-15 23:58:19.806][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-04-15 23:58:19.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.820][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.822][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-04-15 23:58:19.825][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-04-15 23:58:19.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.832][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.835][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:19.837][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:19.839][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.841][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.844][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:19.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 23:58:19.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.853][ef$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:19.855][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:19.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.859][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.862][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-04-15 23:58:19.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-04-15 23:58:19.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.871][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:19.873][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:19.875][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.877][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:19.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 23:58:19.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.887][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:19.890][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:19.891][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.893][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.897][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 23:58:19.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 23:58:19.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.905][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:19.907][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:19.909][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.911][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.914][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-04-15 23:58:19.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-04-15 23:58:19.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.922][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:19.923][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:19.925][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.927][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.930][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-04-15 23:58:19.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-04-15 23:58:19.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:19.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:19.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:19.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:19.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:19.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:19.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:19.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:19.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:20.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 23:58:20.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 23:58:20.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:20.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:20.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:20.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:20.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:20.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:20.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:20.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:20.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:20.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:20.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:20.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:20.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:20.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:20.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:20.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:20.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:20.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:20.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:20.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 23:58:20.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 23:58:20.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 23:58:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 23:58:20.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 23:58:20.094][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-04-15 23:58:20.102][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 23:58:20.105][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-04-15 23:58:20.107][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-04-15 23:58:20.109][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 23:58:20.111][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 23:58:20.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 23:58:20.115][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 23:58:20.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 23:58:20.119][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 23:58:20.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 387 ]
>
> proc.time()
user system elapsed
37.790 2.083 85.450
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 4.555 | 1.123 | 66.520 | |
| ChebiEntry | 0.750 | 0.022 | 0.780 | |