Pierrick Roger
| Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_19 |
| git_last_commit: fad38a4 |
| git_last_commit_date: 2024-04-30 11:37:31 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 200/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.10.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.10.0 |
| 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_1.10.0.tar.gz |
| StartedAt: 2024-10-17 01:48:49 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 01:52:58 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 249.0 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 5.069 2.399 13.196
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-10-17 01:50:45.090][biodb::testContext]
biodb.INFO [2024-10-17 01:50:45.098][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:50:45.102][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-10-17 01:50:45.105][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:50:45.108][biodb::testContext]
biodb.INFO [2024-10-17 01:50:45.124][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:50:45.130][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:50:45.151][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:50:45.154][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:50:45.157][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:50:45.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.172][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:50:45.239][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:50:45.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.244][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.250][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:50:45.254][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:50:45.256][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.259][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.265][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:50:45.268][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:50:45.272][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:50:45.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.302][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:50:45.305][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:50:45.307][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:50:45.309][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.318][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:50:45.321][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:50:45.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.328][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[2024-10-17 01:50:45.331][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:50:45.333][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:50:45.336][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:50:45.339][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.345][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:50:45.349][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:50:45.350][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.358][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:50:45.361][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:50:45.363][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:50:45.365][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.374][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:50:45.377][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:50:45.379][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:50:45.384][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:50:45.388][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:50:45.391][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:50:45.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.401][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[2024-10-17 01:50:45.403][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:50:45.407][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:50:45.410][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.418][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:50:45.421][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:50:45.424][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.432][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:50:45.435][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:50:45.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.444][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:50:45.446][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:50:45.448][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.455][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:50:45.458][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:50:45.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.467][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:50:45.469][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:50:45.491][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:50:45.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.503][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:50:45.505][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:50:45.508][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:50:45.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:45.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:45.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:45.522][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:50:45.629][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.682][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 01:50:45.685][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.687][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:50:45.691][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.694][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.697][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.702][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.705][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:50:45.708][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:50:45.710][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.713][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:50:45.716][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:50:45.718][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.721][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.726][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:50:45.726][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:50:45.726][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:50:45.726][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:50:45.726][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:50:45.729][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:50:45.731][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:45.733][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:45.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:50:45.743][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:45.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:45.748][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.753][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.756][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:50:45.758][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:50:45.760][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.763][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.767][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:50:45.772][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.776][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:50:45.778][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.781][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:50:45.783][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.787][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.790][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.793][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.796][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:50:45.799][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:50:45.802][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.805][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:50:45.807][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:50:45.813][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.815][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.817][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:50:45.817][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:50:45.817][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:50:45.817][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:50:45.817][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:50:45.823][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:50:45.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:45.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:45.831][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:50:45.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:45.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:45.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.844][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.846][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:50:45.850][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:50:45.852][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.854][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.857][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:50:45.864][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.867][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 01:50:45.869][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:50:45.877][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.881][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.885][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.888][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.891][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:50:45.905][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:50:45.908][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.914][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:50:45.917][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:50:45.919][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.922][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.926][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.928][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:50:45.931][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:45.933][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:45.937][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:50:45.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:45.943][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:45.946][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.949][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.951][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:50:45.953][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:50:45.955][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.958][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:45.961][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:50:45.967][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.972][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:50:45.974][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.976][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:50:45.979][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:45.981][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.985][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:45.987][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:50:45.989][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:50:45.992][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:50:45.998][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:46.001][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:50:46.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:50:46.006][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:46.010][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:46.012][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:46.014][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:50:46.017][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:46.021][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:46.023][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:50:46.026][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:46.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:46.034][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:50:46.037][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:46.040][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:50:46.042][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:50:46.046][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:46.049][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:50:46.059][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:50:46.061][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.065][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.093][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.124][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.136][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.146][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[2024-10-17 01:50:46.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.176][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.212][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[2024-10-17 01:50:46.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.234][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.258][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.299][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:50:46.311][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:50:46.315][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:50:46.318][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:50:46.323][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:50:46.329][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:50:46.333][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:50:46.337][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:50:46.343][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:50:46.347][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:50:46.352][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:50:46.356][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:50:46.359][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:50:46.365][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:50:46.368][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:50:46.371][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:50:46.378][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:50:46.381][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:50:46.386][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:50:46.390][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:50:46.393][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:50:46.397][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:50:46.404][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:50:46.408][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:50:46.412][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:50:46.418][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:50:46.422][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:50:46.428][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:50:46.432][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:50:46.435][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:50:46.439][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:50:46.443][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:50:46.447][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:50:46.451][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:50:46.455][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:50:46.459][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:50:46.464][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:50:46.468][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:50:46.472][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:50:46.476][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:50:46.480][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:50:46.485][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:50:46.490][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:50:46.495][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:50:46.556][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:50:46.560][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:50:46.563][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:50:46.568][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:50:46.572][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:50:46.576][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:50:46.579][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:50:46.583][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:50:46.587][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:50:46.590][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:50:46.594][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:50:46.599][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:50:46.602][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:50:46.606][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:50:46.611][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:50:46.616][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:50:46.619][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:50:46.623][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:50:46.626][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:50:46.630][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:50:46.637][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:50:46.640][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:50:46.643][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:50:46.648][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:50:46.653][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:50:46.659][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:50:46.663][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:50:46.667][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:50:46.671][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:50:46.674][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:50:46.678][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:50:46.682][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:50:46.687][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:50:46.691][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:50:46.695][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:50:46.699][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:50:46.702][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:50:46.707][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:50:46.711][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:50:46.730][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:50:46.734][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:50:46.741][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:50:46.743][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.747][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.780][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[2024-10-17 01:50:46.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.818][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.820][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[2024-10-17 01:50:46.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.839][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[2024-10-17 01:50:46.841][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.857][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.871][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[2024-10-17 01:50:46.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.887][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[2024-10-17 01:50:46.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.917][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.931][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:46.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:46.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:46.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:46.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:46.989][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:46.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:46.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:47.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:47.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:47.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:47.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:47.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:47.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:47.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:47.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:47.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:47.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:47.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:47.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:47.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:47.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:47.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:47.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:47.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:47.058][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[2024-10-17 01:50:47.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:47.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:47.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:47.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:47.072][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:47.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:47.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:47.078][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:50:47.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:47.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:47.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:47.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:47.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:47.097][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[2024-10-17 01:50:47.114][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 01:50:47.163][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 01:50:47.171][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:47.175][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:50:47.177][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:47.179][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:50:47.182][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:47.186][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:50:47.189][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:47.191][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 01:50:47.193][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 01:50:47.196][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:50:47.199][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:47.201][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 01:50:47.204][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 01:50:47.209][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 01:50:47.213][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:50:47.215][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:50:47.215][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:50:47.215][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:50:47.220][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 01:50:47.223][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:47.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:47.230][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:50:47.233][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:50:47.238][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:50:47.240][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:50:47.243][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:50:47.243][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 01:50:47.245][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:50:47.249][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:50:47.252][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:50:47.255][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 01:50:47.255][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 01:50:47.276][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:50:47.280][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:50:47.285][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 01:50:47.289][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:50:47.295][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:50:47.300][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:50:47.352][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 01:50:47.359][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 01:50:47.370][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 01:50:47.379][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 01:50:47.388][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:50:47.391][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:50:47.396][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 01:50:47.399][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 01:50:47.425][biodb::testThat]
biodb.INFO [2024-10-17 01:50:47.427][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-10-17 01:50:47.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:47.436][biodb::testThat]
biodb.TRACE[2024-10-17 01:50:47.453][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-10-17 01:50:47.457][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:50:47.470][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:50:47.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:50:47.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:47.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:47.537][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:47.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:47.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:47.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:50:47.565][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:47.567][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:47.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.578][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:47.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:47.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.650][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:47.653][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:47.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.657][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:47.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:47.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.786][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:47.789][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:47.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.804][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.807][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:47.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:47.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.860][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:47.864][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:47.867][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.869][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:47.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:47.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.893][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:47.896][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:47.898][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.900][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:47.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:47.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.916][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:47.918][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:47.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.924][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.927][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:47.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:47.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.939][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:50:47.942][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:47.945][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.948][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.951][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:50:47.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:47.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.968][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:47.970][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:47.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.978][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.981][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:47.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:47.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:47.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:47.992][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:47.994][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:48.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.002][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.006][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:48.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:48.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.019][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:50:48.025][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:48.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.030][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.033][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:50:48.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:48.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.048][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:48.052][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:48.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.059][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.063][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:48.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:48.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:48.322][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-10-17 01:50:48.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:48.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:48.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.341][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:48.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:48.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.494][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:48.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:48.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:48.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:48.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:48.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:48.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.539][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:48.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:48.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.550][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:50:48.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:50:48.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:50:48.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:50:48.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.578][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:50:48.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:50:48.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:50:48.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:50:48.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.647][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.698][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.898][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.900][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.907][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:48.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:48.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.970][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:48.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:48.995][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:48.999][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:49.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.005][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:49.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:49.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:49.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:49.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:49.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:49.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.078][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:49.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:49.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.091][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:49.093][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:49.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.100][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:49.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:49.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.137][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:49.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:49.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:49.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:49.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.166][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:49.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:49.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.177][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:49.180][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:49.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.189][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.192][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:49.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:49.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.273][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.276][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.281][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:49.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.320][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.357][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.359][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.367][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:49.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.404][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:49.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:49.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.415][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:49.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:49.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.425][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:49.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:49.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.454][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:49.456][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:49.459][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.464][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.467][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:49.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:49.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.502][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.515][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.526][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.539][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.541][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.547][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.549][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:49.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.585][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.601][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.613][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.625][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.627][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.629][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.632][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.635][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:49.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.672][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:49.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:49.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:49.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:49.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.698][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:49.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:49.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.712][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:49.715][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:49.717][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.720][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.723][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:49.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:49.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.795][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.798][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.800][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.804][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.807][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:49.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:49.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:49.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:49.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:49.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.884][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:49.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:49.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.898][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:49.901][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:49.903][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.912][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.915][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:49.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.955][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:49.958][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:49.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:49.965][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:49.991][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:49.994][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:49.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.007][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.023][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:50.026][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:50.028][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.035][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.051][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:50.054][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:50.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.062][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.077][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:50.079][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:50.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.085][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.101][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:50.103][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:50.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.112][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.127][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:50.130][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:50.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.139][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.153][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:50.156][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:50.159][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.165][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.181][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-10-17 01:50:50.184][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:50.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.193][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.211][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:50.213][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:50.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.217][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.231][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:50.234][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:50.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.240][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:50:50.265][biodb::testThat]
biodb.INFO [2024-10-17 01:50:50.272][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-10-17 01:50:50.275][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:50.277][biodb::testThat]
biodb.DEBUG[2024-10-17 01:50:50.326][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-10-17 01:50:50.342][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:50:50.353][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-10-17 01:50:50.356][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:50:50.361][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-10-17 01:50:50.364][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:50:50.453][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:50:50.456][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:50:50.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:50:50.462][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:50.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:50.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:50.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:50.487][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:50.489][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:50:50.495][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.498][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.504][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.588][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:50.591][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:50.593][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.596][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.602][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:50.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:50.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.613][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:50.616][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:50.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.622][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.625][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:50.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:50.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.637][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:50.640][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:50.642][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.646][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.650][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:50.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:50.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.662][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:50.666][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:50.668][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.670][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.673][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:50.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:50.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.684][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:50.687][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:50.690][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.692][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.694][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:50.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:50.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.705][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:50:50.708][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:50.711][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.713][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.716][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:50:50.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:50.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.727][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:50.730][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:50.733][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.736][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:50.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:50.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.749][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:50.752][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:50.754][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.757][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.760][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:50.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:50.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.772][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:50:50.776][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:50.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.781][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.783][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:50:50.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:50.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.794][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:50.798][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:50.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.803][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.806][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:50.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:50.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:50.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:50.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.827][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.829][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:50.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:50.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:50.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:50.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.870][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:50.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:50.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:50.926][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-10-17 01:50:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-10-17 01:50:50.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-10-17 01:50:50.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-10-17 01:50:50.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-10-17 01:50:50.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:50.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-10-17 01:50:50.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-10-17 01:50:50.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:50:50.988][biodb::testThat]
biodb.INFO [2024-10-17 01:50:50.990][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-10-17 01:50:50.993][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:50.995][biodb::testThat]
biodb.TRACE[2024-10-17 01:50:51.002][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:51.005][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:51.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:51.010][ef$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:51.013][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-10-17 01:50:51.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:51.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:51.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:51.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:51.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:51.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:51.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:51.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:51.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:51.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:51.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:51.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:51.138][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-10-17 01:50:51.150][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 01:50:51.223][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:50:51.282][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-17 01:50:51.285][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:50:51.288][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-17 01:50:51.368][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[2024-10-17 01:50:51.378][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:50:51.381][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:50:51.398][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:50:52.234][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:50:52.783][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:50:52.787][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-10-17 01:50:52.865][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-10-17 01:50:52.871][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-10-17 01:50:52.901][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:52.923][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:52.926][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:52.928][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:52.930][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:52.933][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:52.935][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:52.937][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:50:52.948][biodb::testThat]
biodb.INFO [2024-10-17 01:50:52.950][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-10-17 01:50:52.953][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:52.955][biodb::testThat]
biodb.TRACE[2024-10-17 01:50:53.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:53.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.027][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:53.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:53.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.038][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:53.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:53.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:53.209][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:50:53.218][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:50:53.221][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 01:50:53.237][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:50:53.240][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-10-17 01:50:53.283][biodb::testThat]
biodb.INFO [2024-10-17 01:50:53.286][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-10-17 01:50:53.289][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:53.291][biodb::testThat]
biodb.TRACE[2024-10-17 01:50:53.346][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:53.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:53.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.357][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:53.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:53.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.410][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.420][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.432][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:50:53.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:50:53.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.444][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:50:53.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:50:53.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.512][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:53.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:53.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:53.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:53.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:53.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:53.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.583][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.593][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-10-17 01:50:53.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.604][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-10-17 01:50:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-10-17 01:50:53.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:53.615][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-10-17 01:50:53.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-10-17 01:50:53.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:53.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:50:53.639][biodb::testThat]
biodb.INFO [2024-10-17 01:50:53.642][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-10-17 01:50:53.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:53.648][biodb::testThat]
biodb.INFO [2024-10-17 01:50:53.670][biodb::testThat]
biodb.INFO [2024-10-17 01:50:53.673][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-10-17 01:50:53.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:53.678][biodb::testThat]
biodb.INFO [2024-10-17 01:50:53.698][biodb::testThat]
biodb.INFO [2024-10-17 01:50:53.701][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-10-17 01:50:53.703][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:53.706][biodb::testThat]
biodb.DEBUG[2024-10-17 01:50:53.716][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-10-17 01:50:54.295][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-10-17 01:50:55.209][biodb::testThat]
biodb.INFO [2024-10-17 01:50:55.212][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-10-17 01:50:55.214][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:55.216][biodb::testThat]
biodb.DEBUG[2024-10-17 01:50:55.669][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[2024-10-17 01:50:56.100][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:56.103][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:56.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.107][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.110][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:56.112][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:56.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.117][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:50:56.120][biodb::testThat]
biodb.INFO [2024-10-17 01:50:56.123][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-10-17 01:50:56.125][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:50:56.127][biodb::testThat]
biodb.TRACE[2024-10-17 01:50:56.152][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:56.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:56.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.162][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:56.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:56.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.171][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:56.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:56.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:56.396][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:50:56.407][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:50:56.410][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 01:50:56.414][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:50:56.419][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 01:50:56.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:50:56.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:50:56.635][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 01:50:56.639][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:50:56.642][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2024-10-17 01:50:56.685][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:50:56.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:50:56.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:56.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:56.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:56.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:56.792][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:50:56.850][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:50:56.853][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:50:56.925][private$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[2024-10-17 01:50:57.322][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[2024-10-17 01:50:57.714][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:50:57.719][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-10-17 01:50:57.728][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-10-17 01:50:57.734][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:50:57.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:57.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:57.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:57.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:57.753][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:57.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:57.758][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-10-17 01:50:57.885][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:50:57.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-10-17 01:50:57.892][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:50:57.894][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:50:57.896][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:50:57.898][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:50:57.901][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:50:57.906][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:50:57.913][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:50:57.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:57.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:57.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:57.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:57.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:57.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:50:57.959][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-10-17 01:50:57.965][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:50:57.967][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:50:57.971][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-10-17 01:50:58.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-10-17 01:50:58.758][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:50:58.763][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-10-17 01:50:58.771][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-10-17 01:50:58.777][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-10-17 01:50:58.781][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:50:58.784][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:50:58.787][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:50:58.790][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:50:58.792][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:50:58.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:50:58.806][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:50:58.808][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:50:58.810][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:50:58.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:50:58.817][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:58.820][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:58.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.824][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:58.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:58.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.836][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:58.839][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:58.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.843][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.846][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:50:58.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:50:58.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.856][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:58.858][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:58.860][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.863][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.866][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:50:58.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:50:58.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.876][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:58.878][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:58.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.882][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:50:58.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:50:58.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.895][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:58.898][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:58.900][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.902][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:50:58.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:50:58.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.914][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:58.917][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:50:58.919][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.922][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.925][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:50:58.928][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:58.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.932][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.935][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:50:58.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:58.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.944][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:58.946][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:58.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.951][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:58.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:50:58.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.963][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:58.966][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:58.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.971][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:50:58.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:50:58.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.984][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:50:58.986][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:58.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:58.990][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:50:58.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:50:59.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.023][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:59.027][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:59.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.032][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.034][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:50:59.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:50:59.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.048][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:59.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:59.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.060][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:59.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:59.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:59.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:59.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.079][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:50:59.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:50:59.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:59.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:59.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:59.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:59.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:59.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:59.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:59.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:59.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:50:59.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:50:59.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:59.163][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-10-17 01:50:59.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:59.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:59.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:59.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:59.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:50:59.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:59.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:50:59.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:50:59.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:50:59.235][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[2024-10-17 01:50:59.244][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:50:59.246][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:50:59.251][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:50:59.650][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:51:00.043][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:00.047][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-10-17 01:51:00.057][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-10-17 01:51:00.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:00.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:00.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:00.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:00.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:00.134][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:00.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:00.139][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:00.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:00.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:00.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:00.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:00.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:00.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:00.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:00.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:00.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:00.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:00.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:00.168][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:00.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:00.172][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:00.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:00.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:00.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:00.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:00.192][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-10-17 01:51:00.194][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:00.198][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-10-17 01:51:00.201][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:00.204][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:00.206][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:00.209][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:00.211][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:00.213][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:00.251][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:00.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:00.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:00.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:00.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:00.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:00.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:00.290][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-10-17 01:51:00.298][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:00.301][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:00.307][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-10-17 01:51:00.698][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-10-17 01:51:01.090][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:01.095][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-10-17 01:51:01.103][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-10-17 01:51:01.109][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-10-17 01:51:01.113][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:01.116][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:01.118][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:01.122][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:01.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:01.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:01.138][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:01.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:01.142][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:01.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:01.149][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.151][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.156][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.181][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:01.184][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:01.186][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.188][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.191][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:01.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:01.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.200][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:01.203][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:01.205][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.207][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.211][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:01.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:01.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.219][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:01.222][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:01.224][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.226][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.228][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:01.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:01.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.238][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:01.240][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:01.242][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.244][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:01.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:01.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.256][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:01.259][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:01.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.263][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.266][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:01.268][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.270][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.272][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.275][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:01.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.284][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:01.288][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:01.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.293][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:01.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:01.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.308][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:01.310][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:01.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.314][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:01.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:01.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.327][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:01.329][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:01.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.334][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.336][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:01.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:01.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.346][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:01.349][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:01.351][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.353][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.356][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:01.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:01.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:01.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:01.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:01.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:01.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:01.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:01.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:01.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:01.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:01.482][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-10-17 01:51:01.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:01.566][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:01.575][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:01.578][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 01:51:01.583][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:01.586][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 01:51:01.594][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:01.596][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:01.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:01.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:01.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:01.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:01.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:01.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:01.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:01.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:01.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:01.658][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:01.660][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:01.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:01.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:01.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:01.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:01.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:01.684][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-10-17 01:51:01.687][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:01.691][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-10-17 01:51:01.694][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:01.697][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:01.699][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:01.702][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:01.705][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:01.708][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:01.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:01.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:01.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:01.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:01.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:01.741][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:01.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:01.746][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-10-17 01:51:01.755][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:01.757][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:01.770][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-10-17 01:51:02.167][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-10-17 01:51:02.560][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:02.565][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-10-17 01:51:02.573][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-10-17 01:51:02.579][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-10-17 01:51:02.582][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:02.585][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:02.588][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:02.591][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:02.593][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:02.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:02.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.609][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:02.616][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.619][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.623][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.634][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:02.636][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:02.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.640][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.643][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:02.645][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:02.647][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.650][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.653][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:02.655][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:02.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.659][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.662][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:02.665][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:02.667][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.669][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.672][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:02.674][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:02.676][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.678][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.681][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:02.683][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.687][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.690][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:02.692][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:02.695][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.697][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.700][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:02.702][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:02.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.706][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.709][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:02.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:02.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.719][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:02.721][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:02.723][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.725][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.728][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:02.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:02.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.738][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:02.740][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:02.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.744][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:02.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:02.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:02.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:02.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:02.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:02.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:02.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:02.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:02.863][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-10-17 01:51:02.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.879][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:02.916][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:02.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:02.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:02.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:02.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:02.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:02.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:02.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:02.947][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:02.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:02.952][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-10-17 01:51:02.954][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:02.960][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-10-17 01:51:02.964][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:02.967][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:02.970][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:02.972][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:02.975][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:02.977][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:02.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:02.988][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:02.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:03.012][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-10-17 01:51:03.020][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:03.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:03.027][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-10-17 01:51:03.420][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-10-17 01:51:03.811][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:03.816][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-10-17 01:51:03.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-10-17 01:51:03.831][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-10-17 01:51:03.835][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:03.838][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:03.841][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:03.845][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:03.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:03.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:03.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:03.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:03.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:03.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:03.873][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:03.875][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:03.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.880][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:03.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:03.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.906][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:03.908][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:03.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.913][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.915][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:03.918][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:03.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.922][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.925][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:03.928][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:03.930][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.933][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.935][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:03.938][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:03.940][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.942][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.945][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:03.948][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:03.950][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.952][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.955][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:03.958][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:03.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.963][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.966][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:03.969][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:03.971][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.973][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.976][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:03.978][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:03.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.983][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:03.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:03.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:03.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:03.997][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:03.999][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:04.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.004][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.007][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:04.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:04.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.017][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:04.020][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:04.025][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.028][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:04.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:04.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:04.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:04.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:04.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:04.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:04.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:04.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:04.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:04.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:04.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:04.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:04.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:04.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:04.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:04.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:04.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:04.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:04.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:04.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:04.139][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-10-17 01:51:04.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:04.221][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:04.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:04.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:04.234][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:04.238][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:04.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:04.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:04.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:04.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.265][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-10-17 01:51:04.268][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:04.273][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-10-17 01:51:04.276][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:04.279][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:04.284][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:04.287][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:04.290][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:04.292][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:04.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:04.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:04.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:04.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:04.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:04.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:04.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:04.332][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-10-17 01:51:04.339][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:04.341][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:04.345][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-10-17 01:51:04.743][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-10-17 01:51:05.207][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:05.211][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-10-17 01:51:05.219][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-10-17 01:51:05.225][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-10-17 01:51:05.228][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:05.231][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:05.234][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:05.237][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:05.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.256][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.258][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.TRACE[2024-10-17 01:51:05.264][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.266][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.271][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.283][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:05.285][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:05.287][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.292][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:05.295][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:05.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.299][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.302][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:05.305][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:05.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.309][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.312][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:05.314][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:05.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.319][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.321][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:05.324][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:05.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.329][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.332][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:05.335][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.337][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.339][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.342][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:05.345][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:05.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.350][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.353][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:05.356][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:05.358][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.360][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:05.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:05.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.387][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:05.389][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:05.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.394][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.396][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:05.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:05.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.406][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:05.408][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:05.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.414][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:05.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:05.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:05.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:05.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:05.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:05.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:05.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:05.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:05.521][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-10-17 01:51:05.524][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.535][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:05.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:05.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:05.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:05.577][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:05.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.605][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-10-17 01:51:05.608][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:05.612][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-10-17 01:51:05.615][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:05.618][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:05.621][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:05.624][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:05.626][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:05.629][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:05.635][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:05.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:05.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:05.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:05.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:05.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:05.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:05.672][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-10-17 01:51:05.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:05.682][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:05.686][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-10-17 01:51:06.080][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-10-17 01:51:06.474][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:06.478][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-10-17 01:51:06.486][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-10-17 01:51:06.493][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-10-17 01:51:06.496][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:06.499][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:06.502][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:06.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:06.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:06.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:06.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:06.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:06.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:06.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:06.533][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.536][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.540][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.552][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:06.555][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:06.557][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.559][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.562][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:06.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:06.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.572][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:06.574][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:06.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.578][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.581][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:06.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:06.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.591][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:06.593][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:06.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.598][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:06.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:06.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.610][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.613][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.615][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.617][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:06.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.630][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.632][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.635][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.637][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.639][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:06.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.649][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:06.651][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.656][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.659][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:06.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.670][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.675][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.678][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.683][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:06.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.695][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:06.698][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:06.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.702][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.706][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:06.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:06.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.716][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:06.719][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:06.721][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.731][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.740][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:06.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:06.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.750][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:06.753][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:06.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.757][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.760][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:06.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:06.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.802][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:06.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:06.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:06.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:06.871][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-10-17 01:51:06.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:06.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:06.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:06.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:06.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:06.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:06.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:06.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:06.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:06.931][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:06.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:06.936][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-10-17 01:51:06.938][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:06.942][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-10-17 01:51:06.947][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:06.950][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:06.953][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:06.957][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:06.960][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:06.962][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:06.970][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:06.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:06.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:06.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:06.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:06.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:06.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:07.001][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-10-17 01:51:07.008][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:07.010][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:07.013][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-10-17 01:51:07.407][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-10-17 01:51:07.806][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:07.811][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-10-17 01:51:07.833][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-10-17 01:51:07.842][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-10-17 01:51:07.845][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:07.849][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:07.852][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:07.856][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:07.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:07.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:07.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:07.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:07.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:07.880][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.TRACE[2024-10-17 01:51:07.885][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.888][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.893][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:07.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:07.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.906][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:07.909][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:07.911][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.914][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.917][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:07.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:07.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.927][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:07.929][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:07.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.933][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.937][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:07.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:07.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.947][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:07.949][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:07.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.954][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.957][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:07.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:07.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.967][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.969][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.974][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:07.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:07.989][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.992][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:07.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:07.997][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.000][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:08.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:08.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.011][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:08.013][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.018][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.021][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:08.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.033][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:08.036][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:08.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.042][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:08.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:08.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.055][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:08.058][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:08.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.063][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.066][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:08.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:08.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.076][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:08.078][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:08.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.083][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.086][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:08.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:08.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.105][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:08.108][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:08.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.117][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:08.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:08.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:08.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:08.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:08.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:08.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:08.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:08.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:08.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:08.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.188][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:08.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:08.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:08.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:08.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:08.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:08.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:08.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:08.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.231][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:08.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:08.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:08.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:08.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:08.254][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-10-17 01:51:08.257][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:08.279][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:08.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:08.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:08.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:08.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:08.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:08.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.317][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-10-17 01:51:08.319][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:08.323][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-10-17 01:51:08.329][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:08.332][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:08.335][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:08.338][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:08.341][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:08.343][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:08.350][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:08.353][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:08.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:08.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:08.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:08.372][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:08.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:08.377][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-10-17 01:51:08.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:08.387][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:08.391][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-10-17 01:51:08.789][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-10-17 01:51:09.184][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:09.189][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-10-17 01:51:09.198][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-10-17 01:51:09.204][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-10-17 01:51:09.211][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:09.214][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:09.217][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:09.221][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:09.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.239][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:09.262][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.264][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.268][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.270][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.282][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:09.285][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:09.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.290][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.293][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:09.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:09.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.302][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:09.305][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:09.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.309][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.312][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:09.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:09.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.322][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:09.325][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:09.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.329][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:09.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:09.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.342][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:09.344][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:09.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.349][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:09.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:09.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.361][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:09.363][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:09.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.367][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.370][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:09.373][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.375][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.377][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.380][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:09.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.389][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:09.392][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:09.394][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.396][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:09.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:09.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.407][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:09.409][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:09.411][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.413][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:09.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:09.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.426][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:09.429][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:09.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.433][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.436][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:09.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:09.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.447][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:09.449][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:09.452][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.455][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.457][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:09.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:09.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:09.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.573][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.583][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:09.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:09.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:09.594][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-10-17 01:51:09.597][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:09.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:09.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:09.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:09.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:09.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.655][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-10-17 01:51:09.658][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:09.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-10-17 01:51:09.666][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:09.668][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:09.671][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:09.673][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:09.676][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:09.678][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:09.684][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:09.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:09.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:09.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:09.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:09.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:09.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:09.714][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-10-17 01:51:09.721][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:09.724][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:09.727][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-10-17 01:51:10.122][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-10-17 01:51:10.515][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:10.519][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-10-17 01:51:10.528][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-10-17 01:51:10.534][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-10-17 01:51:10.538][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:10.541][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:10.544][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:10.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:10.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:10.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:10.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:10.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:10.567][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:10.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:10.574][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.577][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.579][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.581][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.608][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:10.611][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:10.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.615][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:10.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:10.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.629][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:10.632][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:10.634][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.636][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.639][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:10.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:10.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.649][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:10.651][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:10.654][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.656][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:10.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:10.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.669][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.672][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.675][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.677][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.680][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:10.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.691][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.694][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:10.696][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.698][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.701][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:10.703][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.706][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.708][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.711][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:10.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.721][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.724][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.728][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:10.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.740][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:10.743][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:10.745][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.747][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.750][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:10.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:10.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.763][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:10.766][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:10.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.772][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.776][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:10.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:10.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.789][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:10.794][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:10.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.798][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.801][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:10.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:10.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.814][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:10.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.853][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.929][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:10.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:10.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:10.942][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-10-17 01:51:10.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.956][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:10.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:10.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:10.976][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:10.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:10.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:10.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:10.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:11.004][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:11.007][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:11.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:11.012][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-10-17 01:51:11.016][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:11.022][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-10-17 01:51:11.024][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:11.030][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:11.034][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:11.036][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:11.039][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:11.043][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:11.050][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:11.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:11.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:11.071][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:11.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:11.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:11.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:11.081][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-10-17 01:51:11.090][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:11.092][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:11.096][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-10-17 01:51:11.498][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-10-17 01:51:11.890][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:11.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-10-17 01:51:11.903][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-10-17 01:51:11.909][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-10-17 01:51:11.913][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:11.916][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:11.919][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:11.922][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:11.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:11.926][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:11.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:11.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:11.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:11.944][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.TRACE[2024-10-17 01:51:11.949][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.952][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.957][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:11.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:11.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.969][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:11.971][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:11.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.976][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.978][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:11.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:11.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:11.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:11.988][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:11.990][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:11.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.003][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.011][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:12.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:12.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.021][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:12.023][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:12.026][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.028][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:12.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:12.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.041][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.043][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.048][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.050][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:12.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.060][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.063][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:12.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.067][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.070][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:12.072][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.079][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:12.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.089][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.091][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.095][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:12.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.108][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:12.110][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:12.113][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.115][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:12.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.130][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:12.133][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:12.139][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.141][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.144][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:12.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:12.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.157][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:12.161][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:12.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.167][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.169][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:12.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:12.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.203][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:12.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:12.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:12.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:12.300][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-10-17 01:51:12.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:12.333][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:12.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:12.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:12.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:12.350][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:12.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:12.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:12.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:12.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:12.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:12.378][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-10-17 01:51:12.381][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:12.388][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-10-17 01:51:12.391][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:12.394][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:12.398][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:12.401][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:12.403][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:12.406][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:12.414][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:12.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:12.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:12.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:12.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:12.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:12.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:12.445][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-10-17 01:51:12.452][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:12.454][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:12.459][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-10-17 01:51:12.854][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-10-17 01:51:13.246][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:13.251][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-10-17 01:51:13.259][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-10-17 01:51:13.265][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-10-17 01:51:13.268][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:13.271][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:13.274][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:13.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:13.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:13.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:13.292][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:13.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:13.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:13.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:13.303][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.306][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.308][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.322][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:13.325][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:13.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.329][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.331][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:13.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:13.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.341][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:13.343][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:13.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.347][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.350][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:13.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:13.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.359][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:13.362][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:13.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.366][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:13.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.378][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.393][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.396][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.398][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:13.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.411][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:13.413][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:13.415][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.418][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.420][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:13.423][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.434][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.438][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:13.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.448][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:13.450][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:13.453][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.455][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:13.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:13.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.469][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:13.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:13.474][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.477][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:13.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:13.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.503][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:13.512][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:13.515][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.517][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.522][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:13.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:13.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.535][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:13.538][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:13.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.543][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.548][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:13.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:13.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:13.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:13.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:13.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:13.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:13.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:13.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:13.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:13.693][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-10-17 01:51:13.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:13.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:13.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:13.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:13.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:13.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:13.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:13.773][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:13.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:13.777][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:13.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:13.783][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-10-17 01:51:13.785][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:13.789][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-10-17 01:51:13.792][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:13.795][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:13.798][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:13.805][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:13.808][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:13.810][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:13.821][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:13.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:13.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:13.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:13.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:13.848][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:13.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:13.853][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-10-17 01:51:13.865][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:13.867][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:13.875][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-10-17 01:51:14.270][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-10-17 01:51:14.663][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:14.668][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-10-17 01:51:14.676][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-10-17 01:51:14.683][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-10-17 01:51:14.686][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:14.689][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:14.692][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:14.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:14.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:14.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:14.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:14.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:14.714][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:14.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:14.721][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:14.724][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:14.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.729][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:14.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:14.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.741][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:14.744][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:14.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.748][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.751][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:14.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:14.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.761][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:14.764][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:14.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.769][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:14.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:14.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.783][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:14.786][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:14.788][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.790][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:14.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:14.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.803][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:14.806][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:14.808][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.811][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:14.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:14.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.824][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:14.827][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:14.829][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.831][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.834][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:14.850][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:14.853][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.856][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.859][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:14.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.868][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:14.871][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:14.873][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.875][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:14.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:14.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.887][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:14.891][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:14.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.898][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.906][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:14.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:14.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.917][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:14.919][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:14.921][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.923][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.928][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:14.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:14.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.939][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:14.942][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:14.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.946][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.949][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:14.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:14.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:14.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:14.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:14.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:14.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:14.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:14.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:14.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:14.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:15.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:15.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:15.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:15.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:15.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:15.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.041][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:15.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:15.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:15.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:15.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:15.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:15.077][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-10-17 01:51:15.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:15.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:15.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:15.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:15.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:15.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:15.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:15.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:15.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:15.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:15.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:15.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:15.141][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:15.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:15.149][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:15.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:15.154][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-10-17 01:51:15.158][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:15.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-10-17 01:51:15.176][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:15.180][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:15.184][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:15.187][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:15.190][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:15.192][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:15.198][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:15.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:15.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:15.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:15.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:15.229][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:15.232][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:15.245][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-10-17 01:51:15.253][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:15.262][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:15.266][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-10-17 01:51:15.714][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-10-17 01:51:16.108][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:16.112][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-10-17 01:51:16.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-10-17 01:51:16.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-10-17 01:51:16.131][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:16.134][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:16.136][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:16.140][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:16.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:16.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:16.156][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:16.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:16.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:16.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:16.168][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.170][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.172][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.174][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.187][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:16.189][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:16.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.193][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.196][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:16.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:16.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.206][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:16.208][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:16.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.213][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.216][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:16.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:16.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:16.229][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:16.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.234][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.236][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:16.239][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:16.241][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.244][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.247][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:16.249][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:16.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.254][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.257][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:16.260][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.264][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.267][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:16.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.278][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:16.280][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:16.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.285][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:16.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:16.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.300][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:16.304][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:16.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.310][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:16.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.338][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:16.340][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:16.343][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.345][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.348][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:16.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:16.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.357][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:16.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:16.361][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.363][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:16.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:16.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:16.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:16.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:16.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:16.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:16.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:16.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:16.470][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-10-17 01:51:16.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:16.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:16.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:16.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:16.508][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:16.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:16.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:16.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:16.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:16.537][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:16.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:16.541][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-10-17 01:51:16.544][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:16.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-10-17 01:51:16.551][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:16.554][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:16.557][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:16.559][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:16.562][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:16.564][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:16.571][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:16.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:16.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:16.586][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:16.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:16.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:16.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:16.597][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-10-17 01:51:16.604][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:16.607][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:16.612][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-10-17 01:51:17.013][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-10-17 01:51:17.416][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:17.421][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-10-17 01:51:17.429][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-10-17 01:51:17.435][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-10-17 01:51:17.439][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:17.442][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:17.445][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:17.448][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:17.450][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:17.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:17.464][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:17.466][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:17.468][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:17.470][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.TRACE[2024-10-17 01:51:17.475][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.478][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.480][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.482][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.495][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:17.498][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:17.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.502][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.505][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:17.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:17.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.515][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:17.518][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:17.520][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.522][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:17.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:17.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.536][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:17.538][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:17.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.543][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.546][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:17.548][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:17.550][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.553][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.555][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:17.558][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:17.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.562][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.565][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:17.568][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.573][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.576][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:17.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.586][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:17.589][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:17.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.594][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:17.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:17.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.607][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:17.609][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:17.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.614][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.617][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:17.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:17.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.627][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:17.630][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:17.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.634][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.639][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:17.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:17.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.653][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:17.656][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:17.658][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.660][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:17.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:17.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:17.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:17.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.708][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:17.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:17.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:17.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:17.799][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-10-17 01:51:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:17.826][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:17.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:17.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:17.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:17.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:17.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:17.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:17.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:17.861][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:17.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:17.866][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-10-17 01:51:17.869][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:17.875][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-10-17 01:51:17.878][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:17.881][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:17.885][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:17.887][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:17.890][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:17.892][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:17.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:17.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:17.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:17.920][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:17.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:17.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:17.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:17.931][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-10-17 01:51:17.938][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:17.942][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:17.945][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-10-17 01:51:18.345][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-10-17 01:51:18.738][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:18.743][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-10-17 01:51:18.751][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-10-17 01:51:18.757][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-10-17 01:51:18.761][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:18.764][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:18.767][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:18.770][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:18.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:18.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:18.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:18.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:18.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:18.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:18.811][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:18.814][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:18.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.818][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:18.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.831][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:18.834][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:18.836][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.839][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.842][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:18.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:18.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.852][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:18.854][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:18.857][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.859][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:18.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:18.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.872][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:18.874][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:18.877][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.879][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:18.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:18.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.892][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:18.895][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:18.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.899][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.902][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:18.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:18.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.913][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:18.915][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:18.918][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.920][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.923][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:18.928][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:18.931][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.933][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.936][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:18.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:18.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.949][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:18.951][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:18.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.956][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:18.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:18.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.970][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:18.973][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:18.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.978][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.981][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:18.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:18.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:18.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:18.992][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:18.994][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:18.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.000][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.003][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:19.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:19.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.016][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:19.019][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:19.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.025][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.029][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:19.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:19.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:19.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:19.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:19.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:19.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:19.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:19.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:19.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:19.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:19.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:19.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:19.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:19.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:19.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:19.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:19.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:19.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:19.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:19.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:19.169][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-10-17 01:51:19.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:19.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:19.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:19.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:19.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:19.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:19.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:19.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:19.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:19.209][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:19.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:19.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:19.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:19.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:19.231][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:19.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:19.237][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-10-17 01:51:19.239][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:19.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-10-17 01:51:19.247][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:19.249][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:19.252][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:19.255][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:19.258][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:19.260][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:19.266][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:19.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:19.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:19.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:19.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:19.292][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:19.295][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:19.299][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-10-17 01:51:19.306][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:19.308][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:19.314][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-10-17 01:51:19.709][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-10-17 01:51:20.102][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:20.107][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-10-17 01:51:20.115][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-10-17 01:51:20.122][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-10-17 01:51:20.126][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:20.129][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:20.132][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:20.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:20.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:20.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:20.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:20.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:20.157][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:20.159][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[2024-10-17 01:51:20.164][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.171][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.183][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:20.202][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:20.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.207][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.210][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:20.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:20.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.221][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:20.223][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:20.226][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.228][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:20.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:20.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.240][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:20.243][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:20.245][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:20.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:20.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.260][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:20.262][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:20.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.267][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:20.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:20.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.279][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:20.282][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:20.284][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.286][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.288][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:20.291][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.293][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.296][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.299][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:20.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.311][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:20.314][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:20.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.320][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:20.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:20.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.333][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:20.336][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:20.338][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.341][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:20.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:20.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.354][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:20.357][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:20.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.361][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.365][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:20.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:20.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.376][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:20.379][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:20.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.387][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.390][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:20.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:20.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:20.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:20.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:20.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:20.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:20.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:20.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.460][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:20.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:20.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:20.544][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-10-17 01:51:20.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:20.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:20.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:20.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:20.584][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:20.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:20.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:20.601][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:20.608][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:20.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:20.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:20.616][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-10-17 01:51:20.620][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:20.625][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-10-17 01:51:20.628][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:20.632][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:20.635][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:20.637][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:20.640][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:20.644][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:20.650][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:20.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:20.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:20.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:20.674][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:20.676][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:20.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:20.683][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-10-17 01:51:20.694][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:20.696][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:20.699][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-10-17 01:51:21.104][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-10-17 01:51:21.511][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:21.516][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-10-17 01:51:21.525][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-10-17 01:51:21.532][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-10-17 01:51:21.536][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:21.540][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:21.543][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:21.547][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:21.549][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:21.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:21.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:21.565][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:21.568][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:21.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:21.576][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:21.578][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:21.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.583][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:21.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:21.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.594][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.597][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:21.601][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:21.604][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.616][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.619][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:21.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:21.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.647][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:21.662][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:21.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.669][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.672][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:21.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:21.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.734][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:21.740][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:21.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.755][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.759][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:21.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:21.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.779][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:21.781][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:21.783][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.796][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:21.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:21.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.819][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:21.821][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:21.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.839][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.842][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:21.844][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:21.846][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.856][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.860][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:21.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:21.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.881][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:21.884][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:21.901][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.904][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:21.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:21.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.930][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:21.934][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:21.943][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.945][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:21.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:21.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:21.977][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:21.990][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:21.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:21.995][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.009][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:22.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:22.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.029][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:22.032][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:22.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.037][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.047][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:22.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:22.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:22.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:22.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:22.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:22.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:22.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:22.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:22.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:22.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:22.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:22.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:22.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:22.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:22.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:22.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:22.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:22.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:22.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:22.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:22.337][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-10-17 01:51:22.339][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:22.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:22.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:22.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:22.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:22.410][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:22.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:22.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:22.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:22.443][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:22.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:22.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:22.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:22.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:22.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:22.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:22.498][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-10-17 01:51:22.500][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:22.515][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-10-17 01:51:22.518][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:22.521][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:22.523][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:22.539][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:22.541][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:22.544][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:22.561][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:22.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:22.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:22.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:22.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:22.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:22.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:22.612][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-10-17 01:51:22.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:22.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:22.648][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-10-17 01:51:23.050][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-10-17 01:51:23.443][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:23.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-10-17 01:51:23.456][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-10-17 01:51:23.462][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-10-17 01:51:23.466][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:23.469][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:23.472][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:23.476][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:23.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:23.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:23.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:23.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:23.498][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:23.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:23.506][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:23.509][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:23.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.513][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:23.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:23.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.541][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:23.557][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:23.560][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.562][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.565][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:23.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:23.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.578][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:23.580][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:23.582][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.585][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:23.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:23.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.609][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:23.624][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:23.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.629][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.644][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:23.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:23.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.667][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:23.670][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:23.673][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.697][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:23.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:23.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.738][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:23.742][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:23.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.759][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.762][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:23.775][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:23.778][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.780][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.783][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:23.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:23.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.803][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:23.815][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:23.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.819][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:23.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:23.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.846][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:23.860][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:23.862][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.865][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.868][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:23.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:23.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.890][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:23.904][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:23.906][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.909][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.923][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:23.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:23.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.947][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:23.950][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:23.952][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.954][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.969][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:23.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:23.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:23.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:23.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:23.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:23.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:24.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:24.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:24.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:24.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:24.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:24.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:24.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:24.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:24.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:24.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:24.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:24.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:24.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:24.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:24.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:24.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:24.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:24.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:24.257][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-10-17 01:51:24.261][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:24.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:24.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:24.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:24.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:24.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:24.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:24.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:24.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:24.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:24.351][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:24.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:24.415][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:24.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:24.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:24.439][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-10-17 01:51:24.470][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:24.474][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-10-17 01:51:24.478][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:24.492][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:24.495][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:24.498][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:24.517][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:24.520][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:24.526][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:24.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:24.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:24.569][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:24.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:24.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:24.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:24.592][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-10-17 01:51:24.611][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:24.613][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:24.617][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-10-17 01:51:25.031][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-10-17 01:51:25.471][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:25.475][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-10-17 01:51:25.483][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-10-17 01:51:25.489][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-10-17 01:51:25.493][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:25.496][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:25.499][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:25.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:25.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:25.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:25.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:25.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:25.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:25.523][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[2024-10-17 01:51:25.528][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:25.530][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:25.532][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.534][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:25.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:25.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.571][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:25.574][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:25.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.578][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.581][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:25.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.590][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:25.592][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:25.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.597][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.599][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:25.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:25.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.624][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:25.642][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:25.645][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.647][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:25.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:25.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.680][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:25.698][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:25.700][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.703][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:25.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:25.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.734][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:25.737][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:25.739][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.741][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.756][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:25.759][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:25.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.763][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.807][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:25.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:25.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.829][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:25.831][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:25.848][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.851][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:25.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:25.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.878][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:25.881][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:25.894][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.896][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:25.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:25.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.921][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:25.923][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:25.938][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.940][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.943][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:25.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:25.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.967][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:25.970][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:25.986][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:25.988][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:25.991][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:26.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:26.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:26.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:26.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:26.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:26.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:26.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:26.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:26.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:26.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:26.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:26.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:26.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:26.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:26.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:26.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:26.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:26.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:26.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:26.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:26.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:26.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:26.243][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-10-17 01:51:26.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:26.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:26.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:26.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:26.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:26.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:26.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:26.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:26.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:26.329][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:26.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:26.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:26.356][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:26.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:26.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:26.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:26.380][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-10-17 01:51:26.394][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:26.398][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-10-17 01:51:26.401][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:26.416][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:26.419][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:26.443][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:26.446][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:26.462][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:26.473][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:26.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:26.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:26.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:26.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:26.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:26.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:26.539][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-10-17 01:51:26.559][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:26.563][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:26.567][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-10-17 01:51:26.991][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-10-17 01:51:27.389][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:27.393][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-10-17 01:51:27.401][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-10-17 01:51:27.406][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-10-17 01:51:27.410][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:27.413][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:27.415][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:27.419][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:27.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:27.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:27.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:27.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:27.439][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:27.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:27.446][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:27.448][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:27.450][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.452][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:27.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:27.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.464][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:27.466][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:27.468][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.470][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.473][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:27.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:27.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.482][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:27.485][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:27.499][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.501][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.504][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:27.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:27.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.525][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:27.527][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:27.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.543][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:27.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:27.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.565][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:27.568][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:27.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.577][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.580][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:27.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:27.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.601][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:27.604][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:27.618][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.620][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.623][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:27.637][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:27.640][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.643][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.645][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:27.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:27.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.667][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:27.682][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:27.685][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.687][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.690][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:27.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:27.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.751][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:27.754][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:27.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.770][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.774][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:27.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:27.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.798][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:27.800][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:27.816][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.818][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.821][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:27.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:27.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.843][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.845][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:27.847][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:27.861][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.864][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.867][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:27.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:27.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:27.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:27.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:27.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:27.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:27.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:27.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.953][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:27.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:27.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:27.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:27.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:27.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:27.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:28.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:28.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:28.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:28.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:28.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:28.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:28.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:28.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:28.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:28.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:28.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:28.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:28.109][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-10-17 01:51:28.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:28.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:28.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:28.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:28.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:28.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:28.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:28.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:28.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:28.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:28.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:28.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:28.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:28.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:28.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:28.222][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:28.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:28.239][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-10-17 01:51:28.241][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:28.256][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-10-17 01:51:28.260][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:28.262][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:28.265][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:28.280][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:28.283][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:28.285][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:28.305][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:28.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:28.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:28.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:28.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:28.373][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:28.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:28.393][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-10-17 01:51:28.400][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:28.414][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:28.418][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-10-17 01:51:28.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-10-17 01:51:29.248][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:29.253][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-10-17 01:51:29.261][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-10-17 01:51:29.267][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-10-17 01:51:29.271][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:29.274][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:29.276][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:29.279][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:29.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:29.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:29.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:29.297][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:29.299][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:29.301][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:29.306][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:29.309][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:29.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.313][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:29.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:29.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.336][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:29.339][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:29.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.343][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.346][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:29.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:29.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.373][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:29.376][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:29.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.381][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.403][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:29.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:29.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.431][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:29.434][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:29.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.451][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:29.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:29.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.464][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:29.467][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:29.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.497][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:29.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:29.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.527][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:29.530][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:29.543][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.546][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.548][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:29.551][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:29.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.566][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:29.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:29.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.581][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:29.583][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:29.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.605][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.608][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:29.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:29.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.632][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:29.634][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:29.652][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.655][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:29.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:29.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.687][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:29.701][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:29.742][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.745][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.748][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:29.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:29.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.770][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:29.784][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:29.786][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.788][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:29.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:29.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:29.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:29.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.834][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:29.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:29.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:29.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:29.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.879][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:29.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:29.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.900][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:29.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:29.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:29.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:29.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:29.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:29.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:29.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:29.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:29.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:29.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:30.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:30.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:30.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:30.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:30.046][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-10-17 01:51:30.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.070][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:30.214][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:30.234][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:30.246][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 01:51:30.249][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:30.252][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 01:51:30.270][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:30.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:30.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:30.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:30.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:30.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:30.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:30.316][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:30.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:30.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:30.419][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:30.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:30.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:30.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:30.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:30.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:30.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:30.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:30.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:30.614][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:30.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:30.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:30.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:30.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.656][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:30.748][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:30.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:30.752][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:30.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:30.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:30.792][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:30.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:30.797][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:30.903][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:30.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:30.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:30.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:30.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:30.967][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:30.970][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:30.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:30.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:30.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:30.994][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.209][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.237][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.277][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.279][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.314][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.335][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.386][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.399][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.423][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.429][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.515][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.564][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.580][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.585][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.845][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.887][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:31.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:31.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:31.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:31.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:31.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:31.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:31.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:31.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:31.979][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:31.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:31.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:32.021][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:32.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:32.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:32.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:32.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:32.067][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:32.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:32.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.105][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:32.145][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:32.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:32.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:32.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:32.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:32.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:32.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:32.218][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:32.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:32.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:32.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:32.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:32.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:32.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:32.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:32.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.353][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:32.395][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:32.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:32.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:32.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:32.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:32.437][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:32.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:32.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.496][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:32.516][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:32.518][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:32.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:32.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:32.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:32.564][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:32.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:32.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.593][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.615][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:32.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:32.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:32.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:32.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:32.680][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:32.682][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:32.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:32.699][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.720][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:32.785][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:32.788][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:32.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:32.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:32.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:32.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:32.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:32.834][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:32.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:32.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:32.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:32.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:33.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:33.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:33.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:33.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:33.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:33.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:33.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:33.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:33.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:33.248][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:33.268][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:33.271][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:33.278][private$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[2024-10-17 01:51:33.708][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[2024-10-17 01:51:34.106][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:34.111][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-10-17 01:51:34.121][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-10-17 01:51:34.146][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[2024-10-17 01:51:34.155][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:34.158][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:34.163][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:51:34.559][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:51:34.953][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:34.958][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-10-17 01:51:34.968][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-10-17 01:51:34.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:34.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:34.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:34.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:34.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:34.998][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:35.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:35.004][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-10-17 01:51:35.007][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:35.011][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-10-17 01:51:35.014][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:35.017][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:35.021][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:35.024][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:35.027][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:35.044][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:35.053][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:35.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:35.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:35.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:35.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:35.092][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:35.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:35.099][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-10-17 01:51:35.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:35.133][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:35.137][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-10-17 01:51:35.600][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-10-17 01:51:35.992][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:35.996][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-10-17 01:51:36.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-10-17 01:51:36.011][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-10-17 01:51:36.015][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:36.017][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:36.020][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:36.024][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:36.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:36.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:36.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:36.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:36.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:36.045][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.TRACE[2024-10-17 01:51:36.051][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.053][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.057][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.069][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:36.072][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:36.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.076][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.079][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:36.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:36.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.088][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:36.091][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:36.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.095][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.099][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:36.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:36.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.161][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:36.174][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:36.177][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.179][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.182][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:36.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:36.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.205][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:36.208][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:36.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.212][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:36.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.248][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:36.251][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:36.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.255][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.268][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:36.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:36.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.291][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:36.294][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:36.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.299][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.312][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:36.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:36.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.333][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.336][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.341][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.377][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:36.380][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:36.382][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.395][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:36.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:36.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.430][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:36.434][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:36.436][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.439][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.453][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:36.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:36.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.474][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:36.477][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:36.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.494][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.497][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:36.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:36.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:36.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:36.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:36.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:36.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:36.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:36.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.654][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.678][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:36.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:36.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:36.763][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-10-17 01:51:36.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:36.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:36.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:36.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:36.867][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:36.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:36.872][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:36.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:36.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:36.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:36.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:36.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:36.945][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:36.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:36.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:36.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:36.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:36.991][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:36.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:36.996][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-10-17 01:51:37.008][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:37.012][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-10-17 01:51:37.016][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:37.032][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:37.034][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:37.037][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:37.052][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:37.055][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:37.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:37.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:37.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:37.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:37.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:37.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:37.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:37.119][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-10-17 01:51:37.137][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:37.140][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:37.144][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-10-17 01:51:37.581][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-10-17 01:51:37.972][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:37.977][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-10-17 01:51:37.985][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-10-17 01:51:37.992][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-10-17 01:51:37.996][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:51:37.999][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:51:38.002][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:51:38.006][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:38.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:38.010][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:38.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:38.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:38.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:38.029][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.TRACE[2024-10-17 01:51:38.034][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.037][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.050][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.091][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:38.094][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:38.096][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.099][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.115][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:51:38.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:51:38.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.136][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:38.140][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:38.142][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.145][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.158][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:51:38.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:51:38.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.182][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:38.186][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:38.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.191][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:51:38.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:51:38.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.228][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:38.231][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:38.233][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.247][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:51:38.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:51:38.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.275][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:38.278][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:51:38.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.296][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.299][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:38.302][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:38.316][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.319][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.322][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:51:38.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:38.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.347][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.350][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.370][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.395][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:38.397][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:38.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.412][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:51:38.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:51:38.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.438][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:38.440][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:38.455][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.461][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.464][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:51:38.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:51:38.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.488][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:38.491][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:38.505][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.507][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.510][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:51:38.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:51:38.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:38.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:38.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.557][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:38.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:38.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:38.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:38.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.759][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:51:38.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:51:38.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:38.838][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-10-17 01:51:38.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:38.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:38.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:38.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:39.009][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:39.032][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:39.035][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 01:51:39.039][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:39.057][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 01:51:39.064][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:39.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:39.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:39.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:39.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:39.119][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:39.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:39.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:39.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:39.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:39.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:39.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:39.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:39.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:39.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:39.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.334][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.344][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:39.793][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:39.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:39.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:39.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:39.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:39.839][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:39.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:39.843][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.887][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:39.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:39.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:39.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:39.952][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:39.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:39.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:39.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:39.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:39.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:39.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:40.115][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:40.117][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:40.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:40.143][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:40.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:40.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:40.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:40.238][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:40.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:40.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:40.268][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:40.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:40.285][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:40.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:40.357][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:40.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:40.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:40.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:40.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:40.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:40.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.419][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:40.484][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:40.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:40.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:40.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:40.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:40.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:40.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.549][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.571][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.595][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:40.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:40.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:40.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:40.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:40.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:40.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:40.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.685][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.708][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:40.753][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:40.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:40.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:40.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:40.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:40.811][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:40.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:40.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:40.906][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:40.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:40.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:40.948][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:40.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:40.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:40.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:40.978][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:40.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:40.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.003][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:41.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:41.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:41.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:41.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:41.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:41.110][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:41.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:41.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.177][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:41.214][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:41.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:41.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:41.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:41.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:41.269][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:41.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:41.356][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:41.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:41.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:41.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:41.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:41.406][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:41.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:41.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:41.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:41.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:41.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:41.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:41.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:41.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:41.565][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:41.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.619][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:41.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:41.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:41.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:41.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:41.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:41.732][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:41.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:41.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.776][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:41.823][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:41.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:41.838][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:41.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:41.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:41.869][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:41.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:41.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:41.951][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:41.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:41.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:41.971][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:41.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:41.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:42.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:42.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:42.014][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:42.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:42.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.039][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:42.078][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:42.095][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:42.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:42.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:42.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:42.123][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:42.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:42.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:42.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:42.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:42.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:42.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:42.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:42.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:42.266][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:42.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:42.431][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:42.459][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:42.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-10-17 01:51:42.468][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:42.499][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-10-17 01:51:42.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:42.532][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:42.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:42.558][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:42.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:42.562][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:42.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:42.579][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.632][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:42.652][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:42.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:42.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:42.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:42.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:42.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:42.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:42.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:42.803][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:42.805][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:42.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:42.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:42.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:42.846][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:42.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:42.850][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:42.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:42.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:42.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:42.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:42.990][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:42.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.021][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:43.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:43.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:43.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.193][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.198][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.215][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:43.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:43.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:43.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.326][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:43.403][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:43.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:43.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.443][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.445][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.447][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:43.531][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:43.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:43.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.575][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.580][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.623][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:43.644][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:43.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:43.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.688][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.704][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.736][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:43.772][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:43.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:43.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.810][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.813][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:43.888][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:43.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:43.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:43.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:43.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:43.954][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:43.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:43.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:43.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:43.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:43.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.039][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:44.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:44.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:44.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:44.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:44.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:44.210][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:44.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:44.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.250][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.273][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.297][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.299][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:44.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:44.340][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:44.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:44.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.426][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.429][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:44.473][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:44.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:44.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:44.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.515][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.563][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.606][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:44.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:44.611][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:44.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:44.627][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.648][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.669][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.693][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:44.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:44.736][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:44.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:44.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.762][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.797][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.819][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:44.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:44.866][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:44.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:44.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:44.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:44.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:44.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:44.958][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:44.960][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:44.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:44.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:45.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:45.008][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:45.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:45.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:45.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:45.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:45.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:45.151][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:45.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:45.166][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:45.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:45.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.194][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:45.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.345][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:45.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:45.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:51:45.412][biodb::testThat]
biodb.INFO [2024-10-17 01:51:45.426][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-10-17 01:51:45.429][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:45.433][biodb::testThat]
biodb.TRACE[2024-10-17 01:51:45.467][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:45.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:45.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.580][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:45.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:45.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:45.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:45.669][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:45.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:45.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:45.691][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:45.713][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:45.736][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:45.740][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-17 01:51:45.743][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:45.759][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-17 01:51:45.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:45.779][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:45.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:45.813][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:45.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:45.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:45.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:45.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.878][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:45.904][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:45.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:45.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:45.958][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:45.993][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:45.996][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-17 01:51:45.999][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:46.031][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-17 01:51:46.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:46.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:46.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:46.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:46.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:46.096][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:46.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:46.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:46.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:46.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:46.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:46.249][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:46.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:46.255][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:46.258][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:46.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.321][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:46.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:46.340][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:51:46.344][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:46.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:46.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:46.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:46.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:46.394][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:46.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:46.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.442][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.455][private$selectFields]
biodb.TRACE[2024-10-17 01:51:46.457][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:46.459][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:46.462][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.475][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.478][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.483][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.499][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.504][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.510][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.523][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.526][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.528][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.530][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.547][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.550][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:46.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.679][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-17 01:51:46.682][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:46.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:46.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:46.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:46.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:46.725][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:46.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:46.729][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.752][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.774][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.790][private$selectFields]
biodb.TRACE[2024-10-17 01:51:46.793][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:46.795][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:46.798][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.813][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.815][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.818][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.820][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.836][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.840][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.842][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.844][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.858][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.861][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:46.864][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.866][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.883][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.886][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:46.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:46.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:46.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:46.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 01:51:46.968][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:46.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:46.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:46.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:47.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:47.012][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:47.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:47.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.062][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:47.076][private$selectFields]
biodb.TRACE[2024-10-17 01:51:47.078][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:47.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:47.083][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:47.099][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.102][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.107][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.121][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.125][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.128][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.130][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.147][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:47.149][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:47.152][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.172][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.174][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:47.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.210][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:47.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.256][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-17 01:51:47.259][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:51:47.261][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:51:47.319][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:47.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:47.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:47.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:47.737][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:47.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:47.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:47.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:47.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:47.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:47.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:47.801][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:47.819][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:47.821][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:47.837][private$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[2024-10-17 01:51:48.259][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[2024-10-17 01:51:48.660][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:48.664][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-10-17 01:51:48.675][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-10-17 01:51:48.683][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[2024-10-17 01:51:48.691][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:48.694][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:48.699][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:51:49.092][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:51:49.485][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:51:49.490][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-10-17 01:51:49.498][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-10-17 01:51:49.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:49.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:49.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:49.521][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:49.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:49.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:49.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:49.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:49.565][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:49.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:49.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:49.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:49.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:49.600][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:49.602][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:49.604][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:49.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:49.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:49.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:49.688][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:49.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:49.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:49.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:49.719][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:49.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:49.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:49.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:49.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:49.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:49.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:49.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:49.919][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:51:50.066][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:50.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:50.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:50.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:50.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:50.115][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:50.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:50.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.181][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.183][private$selectFields]
biodb.TRACE[2024-10-17 01:51:50.186][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:50.188][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:50.201][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.204][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.207][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.224][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.227][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.229][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.246][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.248][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.251][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.268][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.274][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.291][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:50.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.365][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-17 01:51:50.381][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:50.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:50.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:50.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:50.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:50.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:50.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:50.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.547][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.720][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.723][private$selectFields]
biodb.TRACE[2024-10-17 01:51:50.725][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:50.728][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:50.742][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.745][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.748][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.761][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.765][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.768][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.784][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.791][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.793][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.872][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:50.876][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.879][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.893][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.899][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.902][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:50.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:50.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:50.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.009][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 01:51:51.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:51.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:51.017][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:51.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:51.054][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:51.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:51.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:51.076][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.123][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:51.136][private$selectFields]
biodb.TRACE[2024-10-17 01:51:51.139][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:51.142][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:51.156][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:51.159][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.163][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.182][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.185][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.200][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.203][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.205][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.208][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:51.229][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:51.231][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.235][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.250][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.253][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.256][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:51.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:51.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.356][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-17 01:51:51.370][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:51:51.373][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:51:51.421][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:51.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:51.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:51:51.494][biodb::testThat]
biodb.INFO [2024-10-17 01:51:51.509][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-10-17 01:51:51.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:51.515][biodb::testThat]
biodb.TRACE[2024-10-17 01:51:51.535][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:51.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:51.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.560][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.601][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.632][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:51.698][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:51.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:51.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:51.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:51.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:51.759][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:51.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:51.781][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:51.802][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:51.807][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-17 01:51:51.810][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:51.825][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-17 01:51:51.830][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:51.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:51.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:51.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:51.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:51.879][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:51.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:51.898][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:51.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:51.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:51.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:51.971][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:51.991][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:51.995][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-17 01:51:52.011][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:52.015][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-17 01:51:52.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:52.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:52.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:52.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:52.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:52.080][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:52.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:52.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:52.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:52.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:52.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:52.194][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:52.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:52.199][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:52.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:52.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:52.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:52.289][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:51:52.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:52.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:52.316][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:52.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:52.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:52.400][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:52.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:52.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.439][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.463][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.465][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.481][private$selectFields]
biodb.TRACE[2024-10-17 01:51:52.483][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:52.485][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:52.488][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.504][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.507][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.509][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.512][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.531][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.533][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.536][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.538][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.558][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.561][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.564][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.579][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.583][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.586][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:52.588][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.673][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-17 01:51:52.676][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:52.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:52.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:52.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:52.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:52.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:52.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:52.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.790][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.793][private$selectFields]
biodb.TRACE[2024-10-17 01:51:52.795][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:52.797][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:52.799][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.816][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.819][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.822][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.825][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.842][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.844][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.847][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.849][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.851][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.869][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:52.871][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.873][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.876][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.890][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.892][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:52.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:52.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:52.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:52.976][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 01:51:52.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:52.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:52.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:53.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:53.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:53.022][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:53.024][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:53.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.080][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:53.082][private$selectFields]
biodb.TRACE[2024-10-17 01:51:53.084][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:53.099][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:53.102][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:53.105][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.111][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.127][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.131][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.134][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.143][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.148][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.151][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:53.162][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:53.165][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.167][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.169][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.171][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.184][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:53.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:53.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.249][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-17 01:51:53.252][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:51:53.263][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:51:53.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.329][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:53.409][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:53.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:53.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:53.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:53.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:53.431][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:53.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:53.476][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:53.484][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:53.500][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-17 01:51:53.506][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:53.520][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-17 01:51:53.529][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:53.546][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:53.561][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-17 01:51:53.564][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:53.571][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-17 01:51:53.587][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:53.589][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:53.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:53.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:53.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:53.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:53.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:53.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:53.715][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:53.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:53.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:53.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:53.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:53.761][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:53.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:53.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:53.835][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:53.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:53.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:53.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:53.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:53.878][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:53.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:53.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.922][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:53.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:53.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:53.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:53.947][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:51:53.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:53.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:53.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:53.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:53.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:53.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:54.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:54.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.050][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.064][private$selectFields]
biodb.TRACE[2024-10-17 01:51:54.066][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:54.069][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:54.071][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.086][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.090][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.095][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.101][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.104][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.106][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.109][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.111][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.115][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.117][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.119][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.122][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.125][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:54.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.137][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.153][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-17 01:51:54.155][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:54.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:54.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:54.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:54.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:54.173][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:54.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:54.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.197][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.198][private$selectFields]
biodb.TRACE[2024-10-17 01:51:54.200][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:54.201][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:54.202][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.206][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.208][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.211][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.213][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.215][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.218][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.220][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.222][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.223][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.225][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.226][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.227][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.232][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.237][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:54.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.282][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 01:51:54.286][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:54.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:54.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:54.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:54.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:54.319][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:54.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:54.324][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.347][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.350][private$selectFields]
biodb.TRACE[2024-10-17 01:51:54.352][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:54.354][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:54.355][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.358][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.360][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.362][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.373][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.376][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.378][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.380][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.382][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.385][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:54.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.395][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.398][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.400][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:54.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.451][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:54.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.461][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-17 01:51:54.463][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:51:54.464][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:51:54.481][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:54.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:54.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:51:54.493][biodb::testThat]
biodb.INFO [2024-10-17 01:51:54.495][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-10-17 01:51:54.505][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:54.506][biodb::testThat]
biodb.TRACE[2024-10-17 01:51:54.513][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-10-17 01:51:54.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-10-17 01:51:54.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:54.597][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:54.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:54.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:54.664][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:54.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:54.668][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:54.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:54.680][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:54.686][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:54.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-10-17 01:51:54.692][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:54.695][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-10-17 01:51:54.699][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:54.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:54.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:54.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:54.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:54.747][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:54.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:54.752][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.794][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:54.811][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:54.819][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:54.822][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-10-17 01:51:54.827][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:54.831][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-10-17 01:51:54.836][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:54.839][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:54.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:54.872][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:54.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:54.876][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:54.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:54.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.897][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:54.919][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:54.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:54.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:54.939][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:54.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:54.945][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:54.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:54.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:54.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:51:54.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:54.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:54.976][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:51:54.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:54.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:54.996][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.015][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.019][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:55.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.042][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.044][private$selectFields]
biodb.TRACE[2024-10-17 01:51:55.047][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:55.049][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:55.056][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.059][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.063][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.065][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.077][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.079][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.082][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.085][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.089][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.093][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.095][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.098][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.100][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.110][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.113][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.115][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:55.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.161][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-10-17 01:51:55.163][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.185][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.190][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.192][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:55.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.236][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.238][private$selectFields]
biodb.TRACE[2024-10-17 01:51:55.240][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:55.243][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:55.246][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.248][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.251][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.256][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.266][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.270][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.273][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.275][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.278][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.280][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.282][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.285][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.288][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.298][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.301][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:55.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.336][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 01:51:55.338][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.358][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.360][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:55.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.376][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.378][private$selectFields]
biodb.TRACE[2024-10-17 01:51:55.381][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:55.382][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:55.384][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.389][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.391][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.393][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.395][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.398][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.408][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.411][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.413][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.414][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.416][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.417][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.418][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.420][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:55.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.458][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-10-17 01:51:55.464][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:51:55.466][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:51:55.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.517][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.528][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.537][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:55.555][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.557][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.572][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.574][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:55.582][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:55.591][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:55.593][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-10-17 01:51:55.595][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:55.597][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-10-17 01:51:55.601][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:51:55.607][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:51:55.608][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-10-17 01:51:55.610][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:51:55.612][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-10-17 01:51:55.632][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.649][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:55.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.671][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:55.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.709][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:55.714][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.753][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:55.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.785][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.795][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:55.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:51:55.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:51:55.848][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-10-17 01:51:55.852][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:55.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:55.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:55.865][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:55.866][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:55.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.888][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.898][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.919][private$selectFields]
biodb.TRACE[2024-10-17 01:51:55.921][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:55.922][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:55.923][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.925][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.926][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.927][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.930][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.932][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.935][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.949][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.953][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.956][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.957][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:55.959][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.960][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.961][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.964][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.965][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:55.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:55.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:55.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:55.991][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-10-17 01:51:55.993][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:55.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:55.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:56.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:56.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:56.016][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:56.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:56.026][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.057][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.059][private$selectFields]
biodb.TRACE[2024-10-17 01:51:56.061][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:56.062][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:56.064][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.066][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.068][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.072][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.074][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.077][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.080][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.082][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.084][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.087][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.089][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.092][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.094][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.095][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.098][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:56.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.133][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-10-17 01:51:56.135][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:56.137][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:56.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:56.153][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:56.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:56.156][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:56.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:51:56.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.178][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.180][private$selectFields]
biodb.TRACE[2024-10-17 01:51:56.183][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-10-17 01:51:56.185][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-10-17 01:51:56.187][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.189][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.192][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.204][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.206][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.209][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.212][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.217][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.225][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.228][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.230][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-10-17 01:51:56.232][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.244][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.248][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.251][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-10-17 01:51:56.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:51:56.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:51:56.294][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-10-17 01:51:56.296][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-10-17 01:51:56.305][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-10-17 01:51:56.393][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:56.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-10-17 01:51:56.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:51:56.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-10-17 01:51:56.422][biodb::testThat]
biodb.INFO [2024-10-17 01:51:56.424][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-10-17 01:51:56.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:51:56.437][biodb::testThat]
biodb.DEBUG[2024-10-17 01:51:56.442][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-10-17 01:51:56.444][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:51:56.465][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-10-17 01:51:56.468][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:51:56.470][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:51:56.478][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:51:56.480][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:51:56.483][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:51:56.485][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:51:56.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:51:56.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:51:56.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:51:56.507][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:51:56.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:51:56.522][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:51:56.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:51:56.527][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-10-17 01:51:56.538][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:51:56.540][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:51:56.544][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-10-17 01:52:00.182][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-10-17 01:52:00.580][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2024-10-17 01:52:00.585][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-10-17 01:52:00.590][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-10-17 01:52:00.600][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-10-17 01:52:00.608][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-10-17 01:52:00.612][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:52:00.615][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:52:00.643][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:52:00.680][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:00.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:00.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:00.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:00.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:00.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:00.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:52:00.754][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.757][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.768][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.771][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.802][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:00.804][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:00.812][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.815][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.818][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:00.820][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:00.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.826][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.836][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:52:00.840][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:52:00.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.845][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.849][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:52:00.852][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:52:00.854][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.856][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.859][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:00.862][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:00.864][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.866][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.869][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:00.870][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:00.872][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.874][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.876][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:00.878][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:00.880][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.882][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.885][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:00.887][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:00.890][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.892][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.894][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:00.896][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:00.897][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.898][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.900][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:00.901][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:00.902][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.904][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:00.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:00.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:00.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:00.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.946][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:00.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:00.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.993][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:00.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:00.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:00.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:00.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:01.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:01.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:01.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:01.007][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-10-17 01:52:01.009][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-10-17 01:52:01.024][biodb::testThat]
biodb.INFO [2024-10-17 01:52:01.026][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-10-17 01:52:01.028][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:01.029][biodb::testThat]
biodb.DEBUG[2024-10-17 01:52:01.046][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-10-17 01:52:01.049][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-10-17 01:52:01.050][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-10-17 01:52:01.053][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-10-17 01:52:01.054][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-10-17 01:52:01.056][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:52:01.057][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:52:01.059][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:52:01.062][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:52:01.064][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:52:01.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:01.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:01.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:01.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:01.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:01.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:01.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:01.118][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-10-17 01:52:01.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:01.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:01.126][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-10-17 01:52:01.523][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-10-17 01:52:01.918][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:01.923][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-10-17 01:52:01.931][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-10-17 01:52:01.936][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:01.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:01.940][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:01.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:01.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:01.959][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:01.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:01.965][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-10-17 01:52:01.973][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:01.975][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:01.979][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-10-17 01:52:02.388][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-10-17 01:52:02.786][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:02.791][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-10-17 01:52:02.805][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-10-17 01:52:02.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:02.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:02.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:02.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:02.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:02.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:02.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:02.837][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-10-17 01:52:02.846][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:02.849][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:02.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-10-17 01:52:03.241][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-10-17 01:52:03.654][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:03.659][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-10-17 01:52:03.678][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-10-17 01:52:03.685][private$doSaveContentToFile] Saving to cache [3]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-10-17 01:52:03.702][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:52:03.705][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-10-17 01:52:03.708][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-10-17 01:52:03.721][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:03.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:03.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:03.736][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:03.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:03.740][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:03.742][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.TRACE[2024-10-17 01:52:03.747][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:03.750][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:03.752][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.755][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:03.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:03.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.776][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:03.779][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:03.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.796][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.799][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:03.802][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:03.804][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.822][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.826][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:52:03.828][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:52:03.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.848][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.851][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:52:03.853][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:52:03.870][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.874][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.877][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:03.880][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:03.895][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.898][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.901][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:03.918][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:03.920][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.922][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.925][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:03.939][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:03.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.944][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.947][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:03.966][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:03.968][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:03.971][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:03.988][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:03.992][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:03.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.007][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.010][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:04.013][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:04.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.029][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.032][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:04.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:04.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:04.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:04.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:04.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:04.258][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:04.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:52:04.279][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.281][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.297][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.320][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:04.323][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:04.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.339][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.341][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:04.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:04.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.369][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:04.383][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:04.386][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.389][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:04.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:04.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.415][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:52:04.429][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:52:04.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.434][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.437][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:52:04.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:52:04.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.466][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:52:04.470][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:52:04.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.478][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:52:04.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:52:04.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.525][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:04.528][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:04.530][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.544][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.548][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:04.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:04.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.571][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:04.574][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:04.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.593][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.596][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:04.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:04.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.619][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:04.621][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:04.636][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.638][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:04.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:04.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.666][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:04.680][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:04.682][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.685][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:04.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:04.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.710][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:04.724][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:04.727][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.729][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.754][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:04.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:04.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.776][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:04.779][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:04.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.785][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.802][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:04.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:04.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.875][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:04.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:04.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:04.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:04.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:04.982][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:04.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:04.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:04.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:05.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:05.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:05.027][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:05.029][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.TRACE[2024-10-17 01:52:05.046][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.050][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.058][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.093][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:05.096][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:05.098][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.112][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.115][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:05.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:05.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.136][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:05.138][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:05.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.153][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.157][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:05.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:05.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.180][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:52:05.183][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:52:05.195][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.198][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.201][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:52:05.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:52:05.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.226][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:52:05.288][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:52:05.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.304][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.307][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:52:05.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:52:05.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.330][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:05.333][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:05.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.350][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.355][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:05.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:05.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.391][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:05.395][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:05.398][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.401][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.415][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:05.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:05.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.441][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:05.444][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:05.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.460][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:05.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:05.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.501][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:05.504][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:05.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.509][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:05.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:05.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.552][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:05.555][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:05.567][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.570][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.573][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:05.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:05.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.595][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:05.610][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:05.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.616][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.620][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:05.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:05.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:05.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:05.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.679][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:05.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:05.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.724][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:05.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:05.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.748][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:05.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:05.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:05.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:06.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:06.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:06.017][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-10-17 01:52:06.019][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-10-17 01:52:06.032][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-10-17 01:52:06.097][biodb::testThat]
biodb.INFO [2024-10-17 01:52:06.100][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-10-17 01:52:06.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:06.104][biodb::testThat]
biodb.INFO [2024-10-17 01:52:06.244][biodb::testThat]
biodb.INFO [2024-10-17 01:52:06.247][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-10-17 01:52:06.250][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:06.253][biodb::testThat]
biodb.INFO [2024-10-17 01:52:06.298][biodb::testThat]
biodb.INFO [2024-10-17 01:52:06.309][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-10-17 01:52:06.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:06.314][biodb::testThat]
biodb.DEBUG[2024-10-17 01:52:06.332][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[2024-10-17 01:52:06.352][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:06.355][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:06.360][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:52:06.884][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:52:07.432][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-10-17 01:52:07.435][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-10-17 01:52:07.439][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-10-17 01:52:07.449][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-10-17 01:52:07.478][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:07.480][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:07.483][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:07.485][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:07.487][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:07.489][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:07.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:07.494][ef$get] fields variable is a list.
biodb.INFO [2024-10-17 01:52:07.497][biodb::testThat]
biodb.INFO [2024-10-17 01:52:07.499][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-10-17 01:52:07.501][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:07.504][biodb::testThat]
biodb.ERROR[2024-10-17 01:52:07.548][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-10-17 01:52:07.616][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-10-17 01:52:07.698][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:52:07.701][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 01:52:07.715][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 01:52:07.718][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:52:07.720][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:07.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:07.725][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:07.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:07.745][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:07.748][FUN] Functions in observer BiodbConfig: [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 [2024-10-17 01:52:07.795][biodb::testContext]
biodb.INFO [2024-10-17 01:52:07.798][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:07.811][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-10-17 01:52:07.813][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:07.816][biodb::testContext]
biodb.INFO [2024-10-17 01:52:07.833][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:07.837][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:07.860][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:07.863][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:52:07.865][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:52:07.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:07.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:07.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:07.886][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:52:07.889][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:52:07.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:07.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:07.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:07.911][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:52:07.925][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:52:07.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:07.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:07.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:07.947][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:52:07.950][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:52:07.953][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:52:07.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:07.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:07.971][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:07.975][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:52:07.978][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:52:07.993][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:52:07.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:07.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.014][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:52:08.017][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:52:08.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.037][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:52:08.040][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:52:08.043][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:52:08.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.062][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:52:08.065][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:52:08.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.084][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[2024-10-17 01:52:08.086][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:52:08.099][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:52:08.102][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:52:08.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.126][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:08.164][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:52:08.168][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:52:08.170][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:52:08.173][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:52:08.175][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:52:08.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.196][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:52:08.211][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:52:08.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.234][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:52:08.237][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:52:08.239][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.257][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:52:08.260][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:52:08.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.273][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:52:08.276][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:52:08.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.300][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[2024-10-17 01:52:08.302][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:52:08.305][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:52:08.307][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.344][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:08.346][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:52:08.410][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:52:08.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.418][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[2024-10-17 01:52:08.432][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:52:08.434][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:52:08.439][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:52:08.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:08.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:08.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:08.461][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:52:08.475][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.478][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 01:52:08.480][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.482][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:08.497][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.512][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.516][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.519][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.521][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:08.552][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:08.555][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.557][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:52:08.560][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:08.597][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.599][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.602][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:08.602][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:08.602][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:08.602][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:08.602][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:08.604][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:08.608][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:08.611][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:08.613][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:08.616][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:08.629][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:08.701][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.704][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.719][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:08.724][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:08.726][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.729][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.732][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:52:08.736][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.739][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:08.741][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.743][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:08.746][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.748][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.763][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.765][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.767][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:08.770][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:08.782][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.784][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:52:08.786][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:08.789][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.800][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.813][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:08.813][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:08.813][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:08.813][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:08.813][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:08.816][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:08.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:08.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:08.831][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:08.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:08.836][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:08.839][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.846][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.850][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:08.853][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:08.855][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.858][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.862][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:52:08.868][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.876][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 01:52:08.879][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.881][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:08.884][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.887][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.892][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.898][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.900][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:08.902][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:08.903][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.905][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:52:08.906][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:08.909][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.912][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.914][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.917][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:08.918][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:08.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:08.922][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:08.927][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:08.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:08.930][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.932][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.934][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:08.936][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:08.943][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.945][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.948][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:52:08.955][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.957][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:08.958][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.959][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:08.961][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.963][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.966][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:08.969][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:08.971][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:08.973][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:08.974][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:52:08.978][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:08.980][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.982][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:08.987][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:08.991][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:08.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:08.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:08.995][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:08.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:09.040][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:09.042][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:09.044][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:09.046][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:09.047][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:09.065][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:09.067][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:09.070][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:09.072][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.095][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[2024-10-17 01:52:09.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.120][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.146][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[2024-10-17 01:52:09.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.175][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.200][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[2024-10-17 01:52:09.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.217][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[2024-10-17 01:52:09.223][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.232][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[2024-10-17 01:52:09.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.316][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:09.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:09.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:09.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:09.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:09.332][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:52:09.336][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:52:09.340][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:52:09.351][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:52:09.355][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:52:09.365][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:52:09.369][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:09.373][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:09.388][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:52:09.392][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:52:09.395][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:52:09.433][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:52:09.437][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:09.453][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:09.457][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:52:09.461][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:52:09.482][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:52:09.486][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:52:09.490][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:52:09.505][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:52:09.508][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:52:09.512][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:52:09.534][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:52:09.538][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:52:09.556][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:52:09.560][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:52:09.563][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:52:09.582][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:52:09.585][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:52:09.589][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:52:09.602][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:52:09.606][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:52:09.621][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:52:09.626][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:52:09.629][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:52:09.644][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:52:09.647][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:52:09.651][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:52:09.671][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:52:09.675][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:52:09.679][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:52:09.695][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:52:09.699][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:52:09.713][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:52:09.716][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:52:09.719][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:52:09.734][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:52:09.738][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:52:09.742][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:52:09.759][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:52:09.764][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:52:09.767][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:52:09.783][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:52:09.787][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:52:09.802][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:52:09.807][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:52:09.810][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:52:09.826][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:52:09.830][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:52:09.833][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:52:09.860][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:52:09.887][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:52:09.891][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:52:09.902][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:52:09.909][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:52:09.914][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:52:09.932][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:52:09.936][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:52:09.941][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:52:09.955][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:52:09.959][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:52:09.975][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:52:09.978][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:52:09.982][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:52:09.997][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:52:10.001][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:52:10.005][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:52:10.022][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:52:10.026][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:52:10.041][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:52:10.046][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:52:10.053][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:52:10.067][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:52:10.072][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:52:10.087][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:10.090][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:10.092][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.113][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.157][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[2024-10-17 01:52:10.160][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.186][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.224][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.243][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.336][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.352][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.377][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.383][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.446][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[2024-10-17 01:52:10.451][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.529][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[2024-10-17 01:52:10.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.559][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.635][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:10.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:10.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:10.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:10.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:10.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:10.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:10.803][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:10.806][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 01:52:10.811][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:10.826][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:52:10.828][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:10.831][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:10.833][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:10.836][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:10.838][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:10.852][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 01:52:10.855][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 01:52:10.857][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:10.859][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:10.862][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 01:52:10.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 01:52:10.880][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 01:52:10.883][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:10.898][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:10.898][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:10.898][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:10.900][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 01:52:10.904][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:10.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:10.917][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:10.920][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:10.923][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:10.925][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:10.939][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:52:10.939][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 01:52:10.941][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:10.943][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:10.946][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:10.948][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 01:52:10.948][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 01:52:10.961][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:52:10.966][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:52:10.984][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 01:52:10.988][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:52:10.993][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:52:11.009][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:52:11.027][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 01:52:11.031][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 01:52:11.034][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 01:52:11.050][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 01:52:11.053][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:52:11.055][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:52:11.058][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 01:52:11.075][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 01:52:11.079][biodb::testThat]
biodb.INFO [2024-10-17 01:52:11.081][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-10-17 01:52:11.083][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:11.097][biodb::testThat]
biodb.DEBUG[2024-10-17 01:52:11.105][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 01:52:11.125][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:11.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:11.134][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-10-17 01:52:11.533][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-10-17 01:52:12.047][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:12.052][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-10-17 01:52:12.060][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-10-17 01:52:12.069][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:12.076][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:12.078][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:12.083][private$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[2024-10-17 01:52:12.494][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[2024-10-17 01:52:12.885][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:12.888][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-10-17 01:52:12.895][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-10-17 01:52:12.897][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:12.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:12.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:12.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:12.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:12.923][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:12.925][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[2024-10-17 01:52:12.929][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[2024-10-17 01:52:12.935][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:12.937][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:12.939][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:52:13.340][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:52:13.733][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:13.738][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-10-17 01:52:13.747][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-10-17 01:52:13.751][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:13.753][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:13.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:13.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:13.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:13.770][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:13.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:13.829][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:13.831][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:13.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:13.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:13.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:13.859][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:13.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:13.873][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:13.886][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:52:13.889][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-17 01:52:13.892][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:13.906][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-17 01:52:13.911][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:13.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:13.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:13.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:13.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:13.946][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:13.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:13.966][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:13.984][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:52:14.007][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-17 01:52:14.105][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:14.109][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-17 01:52:14.113][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:14.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:14.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:14.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:14.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:14.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:14.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:14.158][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:14.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:14.162][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:14.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:14.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:14.185][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:14.187][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[2024-10-17 01:52:14.208][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:14.224][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:52:14.228][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-10-17 01:52:14.244][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:14.247][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-10-17 01:52:14.250][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:14.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:14.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:14.283][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:14.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:14.288][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:14.293][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:14.297][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:14.310][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:52:14.313][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-10-17 01:52:14.316][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:14.319][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-10-17 01:52:14.327][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:14.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:14.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:14.348][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:14.350][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:14.360][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:14.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:14.367][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:14.383][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:14.385][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:14.400][private$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[2024-10-17 01:52:14.841][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[2024-10-17 01:52:15.234][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:15.238][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-10-17 01:52:15.247][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-10-17 01:52:15.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:15.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:15.287][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:15.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:15.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:15.301][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:15.303][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.INFO [2024-10-17 01:52:15.318][biodb::testThat]
biodb.INFO [2024-10-17 01:52:15.320][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-10-17 01:52:15.323][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:15.325][biodb::testThat]
biodb.DEBUG[2024-10-17 01:52:15.332][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[2024-10-17 01:52:15.340][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:15.343][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:15.348][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:52:15.746][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:52:16.206][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:16.210][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-10-17 01:52:16.219][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-10-17 01:52:16.224][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:16.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:16.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:16.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:16.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:16.247][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:16.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:16.258][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:16.266][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:16.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:16.273][private$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[2024-10-17 01:52:16.669][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[2024-10-17 01:52:17.063][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:17.068][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-10-17 01:52:17.080][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-10-17 01:52:17.085][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:17.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:17.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:17.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:17.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:17.107][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 01:52:17.121][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:52:17.124][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 01:52:17.127][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 01:52:17.129][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:52:17.132][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:17.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:17.136][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:17.139][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:17.141][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.144][FUN] Functions in observer BiodbConfig: [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 [2024-10-17 01:52:17.175][biodb::testContext]
biodb.INFO [2024-10-17 01:52:17.178][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:17.180][biodb::testContext] Test context - Test web services
biodb.INFO [2024-10-17 01:52:17.193][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:17.196][biodb::testContext]
biodb.INFO [2024-10-17 01:52:17.201][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:17.215][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:17.230][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:17.233][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:52:17.236][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:52:17.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.242][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.245][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:52:17.248][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:52:17.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.264][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.267][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:52:17.281][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:52:17.283][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.302][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:52:17.304][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:52:17.307][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:52:17.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.329][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:52:17.334][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:52:17.348][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:52:17.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.369][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:52:17.372][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:52:17.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.391][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:52:17.394][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:52:17.409][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:52:17.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.430][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:52:17.433][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:52:17.436][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.453][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:52:17.455][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:52:17.469][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:52:17.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.500][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:17.503][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:52:17.506][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:52:17.520][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:52:17.523][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:52:17.526][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:52:17.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.545][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[2024-10-17 01:52:17.559][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:52:17.562][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:52:17.565][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.583][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:52:17.586][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:52:17.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.604][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.606][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:52:17.620][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:52:17.623][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.645][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:52:17.648][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:52:17.651][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.668][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:52:17.671][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:52:17.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.698][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:17.713][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:52:17.741][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:52:17.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.753][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:52:17.756][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:52:17.759][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:52:17.761][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:17.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:17.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:17.777][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:52:17.797][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:17.801][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-10-17 01:52:17.803][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:17.806][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:17.820][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:17.823][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:17.825][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:17.837][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:17.840][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:17.842][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:17.844][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:17.857][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:52:17.859][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:17.862][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:17.866][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:17.879][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:17.879][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:17.879][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:17.879][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:17.879][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:17.883][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:17.886][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:17.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:17.890][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:17.902][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:17.906][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:17.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:17.911][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:17.923][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:17.925][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:17.927][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:17.929][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:17.941][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:52:17.946][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:17.948][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:17.960][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:17.963][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:17.966][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:17.968][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:17.970][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:17.981][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:17.983][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:17.987][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:18.008][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.011][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:52:18.014][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:18.016][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.018][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.034][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:18.034][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:18.034][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:18.034][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:18.034][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:18.037][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:18.039][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:18.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:18.053][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:18.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:18.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:18.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:18.071][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.074][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:18.076][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:18.078][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:18.127][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.132][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:52:18.136][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.139][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-10-17 01:52:18.164][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.166][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:18.169][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.174][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:18.181][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:18.183][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:18.186][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:18.188][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:18.201][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:18.204][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:52:18.206][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:18.209][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.214][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.217][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.219][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:18.221][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:18.230][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:18.232][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:18.234][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:18.236][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:18.239][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:18.246][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.248][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:18.250][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:18.252][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:18.261][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.262][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:52:18.265][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.266][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:18.267][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.268][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:18.270][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.279][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:18.281][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:18.283][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:18.284][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:18.286][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:18.287][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:18.296][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:52:18.298][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:18.301][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.303][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:18.308][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.309][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:18.311][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:18.312][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:18.313][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:18.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:18.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:18.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:18.323][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.325][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:18.326][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:18.327][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:18.328][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:18.330][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:18.331][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.372][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[2024-10-17 01:52:18.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.382][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[2024-10-17 01:52:18.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.434][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.444][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.452][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[2024-10-17 01:52:18.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.509][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.514][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.518][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[2024-10-17 01:52:18.520][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.535][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.537][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[2024-10-17 01:52:18.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.551][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.555][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[2024-10-17 01:52:18.557][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:52:18.560][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:52:18.562][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:52:18.565][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:52:18.568][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:52:18.570][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:52:18.576][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:18.578][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:18.580][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:52:18.583][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:52:18.589][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:52:18.592][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:52:18.595][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:18.599][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:18.602][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:52:18.604][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:52:18.606][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:52:18.608][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:52:18.610][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:52:18.615][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:52:18.619][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:52:18.622][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:52:18.625][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:52:18.628][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:52:18.630][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:52:18.633][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:52:18.634][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:52:18.636][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:52:18.639][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:52:18.646][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:52:18.648][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:52:18.650][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:52:18.651][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:52:18.653][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:52:18.656][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:52:18.659][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:52:18.663][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:52:18.666][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:52:18.668][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:52:18.669][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:52:18.671][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:52:18.674][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:52:18.677][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:52:18.681][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:52:18.688][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:52:18.692][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:52:18.694][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:52:18.698][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:52:18.701][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:52:18.704][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:52:18.714][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:52:18.717][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:52:18.720][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:52:18.724][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:52:18.727][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:52:18.730][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:52:18.734][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:52:18.742][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:52:18.745][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:52:18.757][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:52:18.760][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:52:18.763][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:52:18.766][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:52:18.777][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:52:18.779][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:52:18.781][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:52:18.783][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:52:18.785][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:52:18.799][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:52:18.802][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:52:18.805][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:52:18.807][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:52:18.811][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:52:18.814][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:52:18.817][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:52:18.825][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:52:18.828][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:52:18.831][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:52:18.843][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:52:18.845][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:52:18.848][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:52:18.863][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:52:18.866][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:52:18.869][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:52:18.875][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:18.883][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:18.885][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.889][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:18.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:18.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.910][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[2024-10-17 01:52:18.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:18.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:18.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.925][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:18.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:18.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:18.947][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:18.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:18.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:18.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:18.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:18.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:18.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:18.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:18.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:18.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.107][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[2024-10-17 01:52:19.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.137][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.194][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.232][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[2024-10-17 01:52:19.234][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.259][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[2024-10-17 01:52:19.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.302][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.314][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:19.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:19.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:19.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:19.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:19.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:19.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:19.386][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:19.388][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 01:52:19.393][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:19.396][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:52:19.398][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:19.400][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:19.408][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:19.409][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:19.410][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:19.412][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 01:52:19.413][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 01:52:19.415][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:19.418][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:19.420][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 01:52:19.422][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 01:52:19.425][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 01:52:19.428][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:19.431][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:19.431][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:19.431][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:19.433][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 01:52:19.434][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:19.436][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:19.447][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:19.450][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:19.451][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:19.453][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:19.458][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:52:19.458][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 01:52:19.460][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:19.462][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:19.465][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:19.467][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 01:52:19.467][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 01:52:19.470][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:52:19.474][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:52:19.478][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 01:52:19.484][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:52:19.488][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:52:19.491][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:52:19.500][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 01:52:19.502][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 01:52:19.505][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 01:52:19.508][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 01:52:19.511][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:52:19.517][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:52:19.520][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 01:52:19.522][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 01:52:19.525][biodb::testThat]
biodb.INFO [2024-10-17 01:52:19.528][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-10-17 01:52:19.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:19.534][biodb::testThat]
biodb.DEBUG[2024-10-17 01:52:19.543][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 01:52:19.560][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:52:19.569][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-17 01:52:19.572][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:19.629][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-17 01:52:19.637][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[2024-10-17 01:52:19.645][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:19.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:19.652][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-10-17 01:52:20.114][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-10-17 01:52:20.536][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:20.540][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-10-17 01:52:20.550][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-10-17 01:52:20.564][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:52:20.566][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 01:52:20.568][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 01:52:20.570][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:52:20.577][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:20.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:20.581][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:20.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:20.584][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-10-17 01:52:20.675][biodb::testContext]
biodb.INFO [2024-10-17 01:52:20.678][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:20.680][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-10-17 01:52:20.682][biodb::testContext] ********************************************************************************
biodb.INFO [2024-10-17 01:52:20.693][biodb::testContext]
biodb.INFO [2024-10-17 01:52:20.698][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:20.707][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:20.722][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:20.725][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-10-17 01:52:20.727][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-10-17 01:52:20.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.742][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[2024-10-17 01:52:20.744][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-10-17 01:52:20.746][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-10-17 01:52:20.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.766][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-10-17 01:52:20.777][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-10-17 01:52:20.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.785][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-10-17 01:52:20.786][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-10-17 01:52:20.788][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-10-17 01:52:20.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.796][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-10-17 01:52:20.797][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-10-17 01:52:20.799][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-10-17 01:52:20.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.807][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-10-17 01:52:20.810][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-10-17 01:52:20.812][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.816][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-10-17 01:52:20.817][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-10-17 01:52:20.819][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-10-17 01:52:20.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.825][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[2024-10-17 01:52:20.827][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-10-17 01:52:20.829][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-10-17 01:52:20.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.836][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-10-17 01:52:20.838][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-10-17 01:52:20.840][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-10-17 01:52:20.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.848][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:20.859][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-10-17 01:52:20.862][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-10-17 01:52:20.864][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-10-17 01:52:20.866][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-10-17 01:52:20.873][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-10-17 01:52:20.876][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.886][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-10-17 01:52:20.888][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-10-17 01:52:20.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.895][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-10-17 01:52:20.897][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-10-17 01:52:20.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.908][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-10-17 01:52:20.910][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-10-17 01:52:20.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.922][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-10-17 01:52:20.925][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-10-17 01:52:20.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.936][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-10-17 01:52:20.939][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-10-17 01:52:20.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:20.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:20.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:20.950][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-10-17 01:52:20.952][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-10-17 01:52:21.137][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-10-17 01:52:21.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.140][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.141][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.143][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-10-17 01:52:21.144][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-10-17 01:52:21.145][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-10-17 01:52:21.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.153][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-10-17 01:52:21.158][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.164][self$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[2024-10-17 01:52:21.167][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.169][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:21.171][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.174][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.176][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.178][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.183][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:21.185][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:21.187][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.188][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-10-17 01:52:21.191][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:21.193][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.194][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.197][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:21.197][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:21.197][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:21.197][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:21.197][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:21.205][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:21.207][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.209][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.212][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:21.214][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.224][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.226][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.228][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.229][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:21.230][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:21.232][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.233][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.235][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-10-17 01:52:21.244][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.246][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:21.248][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.249][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:21.251][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.258][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.262][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.264][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.274][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:21.276][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:21.278][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.280][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-10-17 01:52:21.283][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:21.297][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.314][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.317][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:21.317][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:21.317][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:21.317][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-10-17 01:52:21.317][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-10-17 01:52:21.319][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:21.322][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.337][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.340][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:21.342][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.344][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.359][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.362][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.364][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:21.366][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:21.385][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.387][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.390][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-10-17 01:52:21.394][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.396][self$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[2024-10-17 01:52:21.401][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.403][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:21.406][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.409][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.411][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.420][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.423][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-10-17 01:52:21.426][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:21.431][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.434][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-10-17 01:52:21.436][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:21.439][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.456][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.493][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.496][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:21.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.504][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:21.512][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.514][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.516][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.520][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.522][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:21.524][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:21.528][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.531][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.535][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-10-17 01:52:21.538][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.541][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-10-17 01:52:21.548][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:21.553][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.555][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.559][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.561][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.563][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-10-17 01:52:21.566][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:21.568][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.572][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-10-17 01:52:21.574][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:21.577][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:21.583][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.585][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-10-17 01:52:21.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.590][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.592][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:21.595][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:21.597][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:21.599][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:21.602][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.604][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:21.606][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:21.608][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:21.612][self$setPropertyValue]
biodb.DEBUG[2024-10-17 01:52:21.615][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:21.617][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.638][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.641][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.663][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.671][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.707][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.908][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.924][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:21.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.968][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.975][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[2024-10-17 01:52:21.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:21.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:21.989][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:21.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:21.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.002][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.020][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[2024-10-17 01:52:22.023][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-10-17 01:52:22.026][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-10-17 01:52:22.030][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-10-17 01:52:22.041][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-10-17 01:52:22.046][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:52:22.058][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-10-17 01:52:22.061][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:22.064][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:22.074][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-10-17 01:52:22.077][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-10-17 01:52:22.081][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:52:22.091][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-10-17 01:52:22.095][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-10-17 01:52:22.098][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-10-17 01:52:22.116][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-10-17 01:52:22.120][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-10-17 01:52:22.123][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-10-17 01:52:22.148][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-10-17 01:52:22.152][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:52:22.155][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-10-17 01:52:22.171][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-10-17 01:52:22.174][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-10-17 01:52:22.193][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-10-17 01:52:22.197][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-10-17 01:52:22.200][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-10-17 01:52:22.214][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-10-17 01:52:22.217][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-10-17 01:52:22.220][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-10-17 01:52:22.236][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-10-17 01:52:22.240][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-10-17 01:52:22.244][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-10-17 01:52:22.259][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-10-17 01:52:22.263][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-10-17 01:52:22.266][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-10-17 01:52:22.290][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-10-17 01:52:22.293][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-10-17 01:52:22.309][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-10-17 01:52:22.312][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-10-17 01:52:22.316][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-10-17 01:52:22.330][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-10-17 01:52:22.333][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-10-17 01:52:22.336][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-10-17 01:52:22.353][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-10-17 01:52:22.356][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-10-17 01:52:22.360][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-10-17 01:52:22.376][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-10-17 01:52:22.381][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-10-17 01:52:22.385][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-10-17 01:52:22.400][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-10-17 01:52:22.403][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-10-17 01:52:22.417][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-10-17 01:52:22.421][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-10-17 01:52:22.424][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-10-17 01:52:22.428][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-10-17 01:52:22.444][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-10-17 01:52:22.447][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-10-17 01:52:22.453][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-10-17 01:52:22.466][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-10-17 01:52:22.470][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-10-17 01:52:22.474][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-10-17 01:52:22.486][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-10-17 01:52:22.490][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-10-17 01:52:22.501][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-10-17 01:52:22.506][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-10-17 01:52:22.510][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-10-17 01:52:22.532][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-10-17 01:52:22.536][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:52:22.539][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:52:22.555][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-10-17 01:52:22.559][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-10-17 01:52:22.562][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-10-17 01:52:22.575][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-10-17 01:52:22.579][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-10-17 01:52:22.594][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-10-17 01:52:22.598][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-10-17 01:52:22.601][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-10-17 01:52:22.613][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-10-17 01:52:22.617][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-10-17 01:52:22.620][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-10-17 01:52:22.633][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-10-17 01:52:22.636][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-10-17 01:52:22.639][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-10-17 01:52:22.656][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-10-17 01:52:22.661][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-10-17 01:52:22.666][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-10-17 01:52:22.668][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-10-17 01:52:22.670][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.674][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.682][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.795][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.858][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:22.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:22.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:22.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:22.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:22.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:22.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:22.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:23.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:23.053][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.081][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[2024-10-17 01:52:23.084][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.126][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.143][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.DEBUG[2024-10-17 01:52:23.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:23.171][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.188][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:23.209][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.233][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[2024-10-17 01:52:23.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.275][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[2024-10-17 01:52:23.277][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-10-17 01:52:23.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.300][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[2024-10-17 01:52:23.320][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-10-17 01:52:23.324][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-10-17 01:52:23.328][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:23.341][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-10-17 01:52:23.345][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:23.349][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-10-17 01:52:23.352][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:23.368][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-10-17 01:52:23.371][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:23.373][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-10-17 01:52:23.375][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-10-17 01:52:23.377][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-10-17 01:52:23.411][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:23.413][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-10-17 01:52:23.415][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-10-17 01:52:23.417][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-10-17 01:52:23.428][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-10-17 01:52:23.430][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-10-17 01:52:23.430][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-10-17 01:52:23.430][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-10-17 01:52:23.432][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-10-17 01:52:23.435][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:23.437][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:23.450][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-10-17 01:52:23.453][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-10-17 01:52:23.455][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-10-17 01:52:23.458][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-10-17 01:52:23.471][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:52:23.471][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-10-17 01:52:23.474][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-10-17 01:52:23.476][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-10-17 01:52:23.478][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-10-17 01:52:23.490][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-10-17 01:52:23.490][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-10-17 01:52:23.494][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-10-17 01:52:23.498][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-10-17 01:52:23.513][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-10-17 01:52:23.516][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-10-17 01:52:23.528][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-10-17 01:52:23.533][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-10-17 01:52:23.551][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-10-17 01:52:23.554][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-10-17 01:52:23.556][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-10-17 01:52:23.573][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-10-17 01:52:23.576][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:52:23.578][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-10-17 01:52:23.581][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-10-17 01:52:23.596][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-10-17 01:52:23.600][biodb::testThat]
biodb.INFO [2024-10-17 01:52:23.605][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-10-17 01:52:23.621][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-10-17 01:52:23.624][biodb::testThat]
biodb.DEBUG[2024-10-17 01:52:23.632][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-10-17 01:52:23.644][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:52:23.646][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-10-17 01:52:23.647][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:23.649][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-10-17 01:52:23.654][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-10-17 01:52:23.674][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-10-17 01:52:23.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-10-17 01:52:23.691][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-10-17 01:52:23.695][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-10-17 01:52:23.721][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-10-17 01:52:23.724][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-10-17 01:52:23.733][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-10-17 01:52:23.738][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-10-17 01:52:23.740][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-10-17 01:52:23.743][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-10-17 01:52:23.745][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-10-17 01:52:23.747][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-10-17 01:52:23.754][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-10-17 01:52:23.787][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:23.789][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:23.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:23.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:23.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:23.836][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:23.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-10-17 01:52:23.860][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-10-17 01:52:23.867][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-10-17 01:52:23.879][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-10-17 01:52:23.882][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-10-17 01:52:24.301][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-10-17 01:52:25.122][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-10-17 01:52:25.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-10-17 01:52:25.136][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-10-17 01:52:25.143][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-10-17 01:52:25.147][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-10-17 01:52:25.150][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-10-17 01:52:25.153][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-10-17 01:52:25.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-10-17 01:52:25.159][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:25.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:25.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:25.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:25.176][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:25.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-10-17 01:52:25.189][ef$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.191][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.193][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.196][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.208][ef$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:25.210][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:25.213][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.215][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.218][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-10-17 01:52:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-10-17 01:52:25.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.227][ef$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:25.229][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:25.232][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.234][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-10-17 01:52:25.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-10-17 01:52:25.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.256][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-10-17 01:52:25.258][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-10-17 01:52:25.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.271][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.274][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-10-17 01:52:25.277][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-10-17 01:52:25.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.288][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.291][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:25.295][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:25.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.308][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.311][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-10-17 01:52:25.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.329][ef$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:25.331][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:25.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.348][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.351][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-10-17 01:52:25.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-10-17 01:52:25.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.370][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:25.373][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:25.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.388][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:25.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-10-17 01:52:25.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.412][ef$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:25.427][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:25.429][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.431][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.435][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-10-17 01:52:25.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-10-17 01:52:25.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.454][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:25.467][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:25.470][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.472][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.475][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-10-17 01:52:25.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-10-17 01:52:25.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.498][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:25.510][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:25.512][ef$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.514][ef$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.517][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-10-17 01:52:25.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-10-17 01:52:25.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:25.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:25.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:25.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:25.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.582][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-10-17 01:52:25.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-10-17 01:52:25.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.646][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-10-17 01:52:25.737][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-10-17 01:52:25.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-10-17 01:52:25.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-10-17 01:52:25.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-10-17 01:52:25.756][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-10-17 01:52:25.779][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-10-17 01:52:25.788][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-10-17 01:52:25.790][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-10-17 01:52:25.792][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-10-17 01:52:25.794][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-10-17 01:52:25.807][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-10-17 01:52:25.809][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-10-17 01:52:25.811][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-10-17 01:52:25.813][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-10-17 01:52:25.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
41.602 2.257 106.457
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 5.069 | 2.399 | 13.196 | |
| ChebiEntry | 0.839 | 0.022 | 0.957 | |